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NAR Web Server Issue 2006

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Computer Related

DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

Computer Related > Web Services

TavernaTool Content

http://taverna.sourceforge.net/

Computer Related > Web Services
DNA > Annotations
DNA > Gene Prediction
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Taverna is a tool for creating and running bioinformatics workflows.

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tagscomputational biology database management systems genetic databases genomics online systems sequence analysis software design systems integration
setsUniversity of Manchester

DNA > Annotations

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

KOBASTool Content

http://kobas.cbi.pku.edu.cn

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

TACTTool Content

http://jbirc.jbic.or.jp/tact/

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

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tagsalternative splicing amino acid motifs amino acid sequence base sequence complementary dna computational biology dna sequence analysis expressed sequence tags genes genetic databases genetic models genetic polymorphism genetic transcription human genome humans messenger rna microsatellite repeats molecular sequence data nucleic acid databases open reading frames protein databases proteins rna sequence analysis sequence analysis single nucleotide polymorphism systems integration tertiary protein structure

TavernaTool Content

http://taverna.sourceforge.net/

Computer Related > Web Services
DNA > Annotations
DNA > Gene Prediction
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Taverna is a tool for creating and running bioinformatics workflows.

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tagscomputational biology database management systems genetic databases genomics online systems sequence analysis software design systems integration
setsUniversity of Manchester

WEGOTool Content

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Protein > Annotation and Function

Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram.

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tagscontrolled vocabulary genes genomics

DNA > DNA and Genomic Analysis

Virtual RibosomeTool Content

http://www.cbs.dtu.dk/services/VirtualRibosome/

DNA > DNA and Genomic Analysis
DNA > Gene Prediction

The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results.

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tagsanimals dna sequence analysis exons initiator codon introns open reading frames protein biosynthesis ribosomes systems integration terminator codon

DNA > Gene Prediction

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

DNA > Gene Prediction
Model Organisms > Microbes

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

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tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

TACTTool Content

http://jbirc.jbic.or.jp/tact/

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

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tagsalternative splicing amino acid motifs amino acid sequence base sequence complementary dna computational biology dna sequence analysis expressed sequence tags genes genetic databases genetic models genetic polymorphism genetic transcription human genome humans messenger rna microsatellite repeats molecular sequence data nucleic acid databases open reading frames protein databases proteins rna sequence analysis sequence analysis single nucleotide polymorphism systems integration tertiary protein structure

TavernaTool Content

http://taverna.sourceforge.net/

Computer Related > Web Services
DNA > Annotations
DNA > Gene Prediction
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Taverna is a tool for creating and running bioinformatics workflows.

NAR Web Server Issue 2006
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tagscomputational biology database management systems genetic databases genomics online systems sequence analysis software design systems integration
setsUniversity of Manchester

TiCoTool Content

http://tico.gobics.de/

DNA > Gene Prediction
Model Organisms > Microbes

TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER.

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tagsalgorithms artificial intelligence automated pattern recognition bacterial genome base sequence cluster analysis dna sequence analysis genomics initiator codon molecular sequence data prokaryotic cells prokaryotic initiation factors protein biosynthesis translational peptide chain initiation

Virtual RibosomeTool Content

http://www.cbs.dtu.dk/services/VirtualRibosome/

DNA > DNA and Genomic Analysis
DNA > Gene Prediction

The Virtual Ribosome is a DNA translation tool with a built-in ORF finder that allows the use of alternative start codons, the IUPAC degenerate DNA alphabet, and all translation tables defined by the NCBI taxonomy group. The tool can also highlight the intron/exon structure of genes using information found in the feature table of GenBank flatfiles in the final translation results.

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tagsanimals dna sequence analysis exons initiator codon introns open reading frames protein biosynthesis ribosomes systems integration terminator codon

DNA > Mapping and Assembly

EGassemblerTool Content

http://egassembler.hgc.jp

DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE

EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.

This content is being maintained by amasoudin.

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tagscomputational biology dna sequence analysis expressed sequence tags genomics

DNA > Phylogeny Reconstruction

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

ModelTest SeverTool Content

http://darwin.uvigo.es/software/modeltest_server.html

DNA > Phylogeny Reconstruction

ModelTest is program for the selection the model of DNA evolution (nucleotide substitution) that best fits your data from phylogenetic analyses.

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tagsalgorithms base composition bayes theorem biological models dna dna sequence analysis genetic variation likelihood functions molecular evolution nucleotides online systems sequence alignment statistical models

NASTTool Content

http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
RNA > General Resources
Sequence Comparison > Multiple Sequence Alignments

Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

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tagsalgorithms archaeal genes bacillus anthracis bacterial genes cluster analysis computer-aided design dna probes dna sequence analysis equipment design gene expression profiling nucleic acid sequence homology oligonucleotide array sequence analysis ribosomal rna rrna genes sequence alignment staphylococcus aureus

PAL2NALTool Content

http://coot.embl.de/pal2nal/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.

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tagscodon dna sequence analysis exons protein sequence analysis sequence alignment

SPRINGTool Content

http://algorithm.cs.nthu.edu.tw/tools/SPRING

DNA > Phylogeny Reconstruction
Sequence Comparison > Comparative Genomics

Sorting Permutation by Reversals and Block Interchanges (SPRING) is a tool for the analysis of genome rearrangements. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges for transforming one chromosome into another. Phylogenetic trees based on the rearrangement analysis are also shown as part of the results.

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tagsalgorithms bacterial chromosomes bacterial genome chromosome inversion chromosome mapping chromosomes dna sequence analysis gammaproteobacteria gene order gene rearrangement genetic models genetic recombination genomics molecular evolution nucleic acid sequence homology phylogeny sequence alignment vibrio

SWAKKTool Content

http://oxytricha.princeton.edu/SWAKK/

DNA > Phylogeny Reconstruction
Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Sequence Comparison > Pairwise Sequence Alignments

Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.

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tagsamino acid substitution computational biology dna sequence analysis genetic selection protein conformation proteins sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

TreeDomViewerTool Content

http://www.bioinformatics.nl/tools/treedom

DNA > Phylogeny Reconstruction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

TreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment.

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tagsphylogeny protein sequence analysis proteins sequence alignment software design tertiary protein structure

DNA > Sequence Polymorphisms

FastSNPTool Content

http://fastsnp.ibms.sinica.edu.tw

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Function Analysis and Selection Tool for Single Nucleotide Polymorphisms (FastSNP) allows users to identify and prioritize SNPs that are likely to have functional effects.

This content is being maintained by fastsnp.

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tagsgene frequency genetic predisposition to disease phenotype proteins risk single nucleotide polymorphism

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.

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tagsalgorithms cluster analysis drug dose-response relationship gene expression profiling genetic polymorphism kinetics oligonucleotide array sequence analysis systems integration

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

PDATool Content

http://pda.uab.es/pda2/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Sequence Comparison > Analysis of Aligned Sequences

PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.

This content is being maintained by soniacas.

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tagsalgorithms animals dna sequence analysis drosophila genetic polymorphism nucleic acid databases sequence alignment

PupaSuiteTool Content

http://pupasuite.bioinfo.cipf.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.

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tagsalgorithms amino acid substitution binding sites genetic transcription genotype haplotypes humans linkage disequilibrium molecular evolution nucleic acid databases phenotype rna splicing single nucleotide polymorphism transcription factors

SNP@DomainTool Content

http://snpnavigator.net/

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Domains and Motifs

SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.

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tagshumans protein databases protein sequence analysis single nucleotide polymorphism tertiary protein structure

SNPmaskerTool Content

http://bioinfo.ebc.ee/snpmasker/

DNA > Sequence Polymorphisms
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Expression > Transcript Expression Analysis
Human Genome > Sequence Polymorphisms

SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.

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tagsalleles animals dna primers genomics human genome humans mice nucleic acid databases nucleic acid probes nucleic acid repetitive sequences single nucleotide polymorphism

SVMHCTool Content

http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/

DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.

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tagsalleles animals artificial intelligence computational biology histocompatibility antigens histocompatibility antigens class i hla antigens humans mice peptides predictive value of tests protein binding protein databases protein sequence analysis sensitivity and specificity single nucleotide polymorphism t-lymphocyte epitopes

DNA > Sequence Retrieval and Submission

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

DNA > Structure and Sequence Feature Detection

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

CEASTool Content

http://ceas.cbi.pku.edu.cn

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

NAR Web Server Issue 2006
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tagsbinding sites chromatin immunoprecipitation genomics human genome humans oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

CMATool Content

http://www.gene-regulation.com/pub/programs/cma/CMA.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

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tagsalgorithms amino acid sequence binding sites chemical models computer simulation dna sequence analysis endothelial cells gene expression profiling genetic promoter regions humans molecular sequence data protein binding protein sequence analysis transcription factors

CRSDDatabase Content

http://140.120.213.10:8080/crsd/main/home.jsp

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
RNA > Functional RNAs

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

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tags3' untranslated regions binding sites cluster analysis gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics humans micrornas oligonucleotide array sequence analysis transcription factors

CorGenTool Content

http://corgen.molgen.mpg.de

DNA > Structure and Sequence Feature Detection

CorGenmeasures long-range correlations in DNA sequences and can generate random sequences with the same (or user-specified) correlation and composition parameters.

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tagsalgorithms base composition computational biology cytosine dna sequence analysis genomics guanine humans sequence alignment statistical data interpretation

FeatureScanTool Content

http://gnaweb.gbf.de/cgi-bin/FeatureScan/FeatureScan.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Similarity Searching

FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.

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tagsanimals automated pattern recognition bacterial dna bacterial genes dna dna sequence analysis escherichia coli genetic models genetic promoter regions genomics humans mice nucleic acid sequence homology rats sequence alignment thermodynamics

GC-ProfileTool Content

http://tubic.tju.edu.cn/GC-Profile/

DNA > Structure and Sequence Feature Detection

GC-Profile is a web-based tool for visualizing and analyzing the variation of GC content in genomic sequences.

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tagsalgorithms animals archaeal genome automated pattern recognition bacterial genome base composition base sequence chickens chromosome mapping cpg islands cytosine dna dna sequence analysis genetic models genomic islands genomics guanine isochores molecular sequence data sequence alignment statistical models

GenDecoderTool Content

http://darwin.uvigo.es/software/gendecoder.html

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Multiple Sequence Alignments

GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.

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tagsamino acid sequence animals base sequence codon conserved sequence mitochondrial genes molecular evolution protein biosynthesis sequence alignment sequence analysis

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

MoD ToolsTool Content

http://159.149.109.16/modtools/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

NAR Web Server Issue 2006
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tagsbinding sites dna sequence analysis gene expression regulation nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna sequence analysis transcription factors transcriptional regulatory elements untranslated rna

NXSensorTool Content

http://www.sfu.ca/~ibajic/NXSensor/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.

NAR Web Server Issue 2006
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tagsbinding sites dna dna sequence analysis dna-binding proteins genetic promoter regions nucleic acid conformation nucleosomes transcription factors

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

POXOTool Content

http://www.bioinfo.biocenter.helsinki.fi/poxo

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.

This content is being maintained by mkankain.

NAR Web Server Issue 2006
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tagsarabidopsis binding sites cluster analysis computational biology dna sequence analysis down-regulation gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics hydrogen peroxide itraconazole oligonucleotide array sequence analysis reproducibility of results software design statistical data interpretation transcription factors transcriptional regulatory elements up-regulation

PlotRepTool Content

http://repeats.abc.hu/cgi-bin/plotrep.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

PlotRep is a tool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphical output.

NAR Web Server Issue 2006
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tagsgenomics interspersed repetitive sequences

QGRS MapperTool Content

http://bioinformatics.ramapo.edu/QGRS/index.php

DNA > Structure and Sequence Feature Detection
Expression > Splicing
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

NAR Web Server Issue 2006
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tagsdna dna sequence analysis g-quadruplexes guanine oligonucleotides rna rna sequence analysis

QuadFinderTool Content

http://miracle.igib.res.in/quadfinder/

DNA > Structure and Sequence Feature Detection
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences.

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tagsdna dna sequence analysis g-quadruplexes guanine rna rna sequence analysis

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

RegRNATool Content

http://regrna.mbc.nctu.edu.tw/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Splicing
RNA > Functional RNAs
RNA > Motifs

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

NAR Web Server Issue 2006
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tagsanimals humans messenger rna mice nucleic acid conformation nucleic acid sequence homology rats ribonucleic acid regulatory sequences rna sequence analysis systems integration untranslated regions

SNPmaskerTool Content

http://bioinfo.ebc.ee/snpmasker/

DNA > Sequence Polymorphisms
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Expression > Transcript Expression Analysis
Human Genome > Sequence Polymorphisms

SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.

NAR Web Server Issue 2006
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tagsalleles animals dna primers genomics human genome humans mice nucleic acid databases nucleic acid probes nucleic acid repetitive sequences single nucleotide polymorphism

TACTTool Content

http://jbirc.jbic.or.jp/tact/

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

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tagsalternative splicing amino acid motifs amino acid sequence base sequence complementary dna computational biology dna sequence analysis expressed sequence tags genes genetic databases genetic models genetic polymorphism genetic transcription human genome humans messenger rna microsatellite repeats molecular sequence data nucleic acid databases open reading frames protein databases proteins rna sequence analysis sequence analysis single nucleotide polymorphism systems integration tertiary protein structure

TFBSclusterTool Content

http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources
Model Organisms > Mouse and Rat

TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.

NAR Web Server Issue 2006
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tagsalgorithms animals base sequence binding sites chromosome mapping cluster analysis conserved sequence dna sequence analysis gene expression profiling gene expression regulation genetic promoter regions genetic transcription genomics humans mice molecular sequence data nucleic acid sequence homology protein binding sequence alignment transcription factors transcriptional regulatory elements

VOMBATTool Content

https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jsp

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.

NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence bayes theorem binding sites chemical models computer simulation genomics markov chains molecular models protein binding protein databases protein sequence analysis sequence alignment statistical models structure-activity relationship transcription factors transcriptional regulatory elements

Zinc Finger ToolsTool Content

http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

NAR Web Server Issue 2006
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tagsamino acid sequence animals base sequence binding sites biomolecular nuclear magnetic resonance cell line combinatorial chemistry techniques computer simulation deoxyribonuclease i deoxyribonucleases dna dna primers dna sequence analysis dna-binding proteins down-regulation drug design enzyme-linked immunosorbent assay epidermal growth factor receptor erbb genes erbb-1 genes erbb-2 genes erbb-2 receptor erbb-3 receptor flow cytometry gene expression profiling gene expression regulation gene library gene targeting genetic promoter regions genetic transcription green fluorescent proteins histidine human genome humans kidney luminescent proteins lysine mice molecular cloning molecular models molecular sequence data mutation nucleic acid conformation oligonucleotides peptide library pliability polymerase chain reaction protein conformation protein engineering proteomics recombinant proteins reporter genes retroviridae secondary protein structure sequence analysis site-directed mutagenesis substrate specificity tertiary protein structure transcription factors transfection up-regulation x-ray crystallography zinc fingers

iCRTool Content

http://210.212.215.199/icr/index.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Interactions, Pathways, Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

NAR Web Server Issue 2006
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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

jPREdictorTool Content

http://bibiserv.techfak.uni-bielefeld.de/jpredictor/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.

NAR Web Server Issue 2006
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tagsanimals binding sites drosophila melanogaster drosophila proteins genomics response elements transcription factors transcriptional regulatory elements

DNA > Tools For the Bench

DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/

DNA > Tools For the Bench
Human Genome > Health and Disease

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

NAR Web Server Issue 2006
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tagscodon computational biology cpg islands dna primers dna vaccines drug design gene expression polymerase chain reaction restriction mapping systems integration

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE
Model Organisms > Plants

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

NAR Web Server Issue 2006
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tagsbase sequence conserved sequence dna primers expressed sequence tags fabaceae genetic markers genetic polymorphism genomics nucleic acid databases poaceae polymerase chain reaction sequence alignment

MutScreenerTool Content

http://bioinfo.bsd.uchicago.edu/MutScreener.html

DNA > Tools For the Bench

MutScreener is a human-specific primer design tool that considers gene annotation information to design primers for mutation screening. Users can provide custom gene annotation or use existing public gene annotations.

NAR Web Server Issue 2006
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tagsdna primers exons genetic promoter regions genomics human genome humans polymerase chain reaction

PrimerStationTool Content

http://ps.cb.k.u-tokyo.ac.jp/

DNA > Tools For the Bench
Human Genome > Other Resources

PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.

NAR Web Server Issue 2006
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tagsdna primers genomics human genome humans polymerase chain reaction temperature

SNPmaskerTool Content

http://bioinfo.ebc.ee/snpmasker/

DNA > Sequence Polymorphisms
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Expression > Transcript Expression Analysis
Human Genome > Sequence Polymorphisms

SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.

NAR Web Server Issue 2006
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tagsalleles animals dna primers genomics human genome humans mice nucleic acid databases nucleic acid probes nucleic acid repetitive sequences single nucleotide polymorphism

siVirusTool Content

http://sivirus.rnai.jp/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Other Organisms
RNA > Structure Prediction, Visualization, and Design

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.

NAR Web Server Issue 2006
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tagsanti-hiv agents antiviral agents base sequence conserved sequence genetic variation rna interference rna viruses small interfering rna viral rna

Education > Directories and Portals

Bioinformatics Links DirectoryResource Content

http://www.bioinformatics.ca/links_directory/

Education > Directories and Portals

The Bioinformatics Links Directory features curated links to molecular resources, tools and databases. All of the resources are free or available for a nominal fee.

This content is being maintained by Francis Ouellette.

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external linksLink on TwitterLink on Wikipedia
tagscomputational biology directories as topic factual databases genetic databases genetics humans molecular biology
setsOntario Institute for Cancer Research (OICR)

Expression > Gene Regulation

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

CEASTool Content

http://ceas.cbi.pku.edu.cn

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

NAR Web Server Issue 2006
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tagsbinding sites chromatin immunoprecipitation genomics human genome humans oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

CMATool Content

http://www.gene-regulation.com/pub/programs/cma/CMA.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence binding sites chemical models computer simulation dna sequence analysis endothelial cells gene expression profiling genetic promoter regions humans molecular sequence data protein binding protein sequence analysis transcription factors

CRSDDatabase Content

http://140.120.213.10:8080/crsd/main/home.jsp

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
RNA > Functional RNAs

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

NAR Web Server Issue 2006
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tags3' untranslated regions binding sites cluster analysis gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics humans micrornas oligonucleotide array sequence analysis transcription factors

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

NAR Web Server Issue 2006NAR Web Server Issue 2009
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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

MoD ToolsTool Content

http://159.149.109.16/modtools/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

NAR Web Server Issue 2006
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tagsbinding sites dna sequence analysis gene expression regulation nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna sequence analysis transcription factors transcriptional regulatory elements untranslated rna

NXSensorTool Content

http://www.sfu.ca/~ibajic/NXSensor/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Nucleosome eXclusion Sensor (NXSensor) finds potential nucleosome-free regions of DNA sequences. NXSensor can be used to assess the likelihood of nucleosome formation in regions involved in gene regulation and other aspects of chromatin function.

NAR Web Server Issue 2006
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tagsbinding sites dna dna sequence analysis dna-binding proteins genetic promoter regions nucleic acid conformation nucleosomes transcription factors

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

POXOTool Content

http://www.bioinfo.biocenter.helsinki.fi/poxo

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.

This content is being maintained by mkankain.

NAR Web Server Issue 2006
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tagsarabidopsis binding sites cluster analysis computational biology dna sequence analysis down-regulation gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics hydrogen peroxide itraconazole oligonucleotide array sequence analysis reproducibility of results software design statistical data interpretation transcription factors transcriptional regulatory elements up-regulation

RNAhybridTool Content

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Expression > Gene Regulation
RNA > Functional RNAs

RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.

NAR Web Server Issue 2006
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tags3' untranslated regions algorithms animals binding sites body patterning caenorhabditis elegans caenorhabditis elegans proteins computational biology drosophila homeodomain proteins insect genes messenger rna micrornas nucleic acid conformation nucleic acid databases post-transcriptional rna processing rna interference thermodynamics

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

NAR Web Server Issue 2006
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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

RegRNATool Content

http://regrna.mbc.nctu.edu.tw/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Splicing
RNA > Functional RNAs
RNA > Motifs

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

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tagsanimals humans messenger rna mice nucleic acid conformation nucleic acid sequence homology rats ribonucleic acid regulatory sequences rna sequence analysis systems integration untranslated regions

TFBSclusterTool Content

http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources
Model Organisms > Mouse and Rat

TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.

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tagsalgorithms animals base sequence binding sites chromosome mapping cluster analysis conserved sequence dna sequence analysis gene expression profiling gene expression regulation genetic promoter regions genetic transcription genomics humans mice molecular sequence data nucleic acid sequence homology protein binding sequence alignment transcription factors transcriptional regulatory elements

VOMBATTool Content

https://www2.informatik.uni-halle.de:8443/VOMBAT/faces/pages/choose.jsp

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.

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tagsalgorithms artificial intelligence bayes theorem binding sites chemical models computer simulation genomics markov chains molecular models protein binding protein databases protein sequence analysis sequence alignment statistical models structure-activity relationship transcription factors transcriptional regulatory elements

Zinc Finger ToolsTool Content

http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.

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tagsamino acid sequence animals base sequence binding sites biomolecular nuclear magnetic resonance cell line combinatorial chemistry techniques computer simulation deoxyribonuclease i deoxyribonucleases dna dna primers dna sequence analysis dna-binding proteins down-regulation drug design enzyme-linked immunosorbent assay epidermal growth factor receptor erbb genes erbb-1 genes erbb-2 genes erbb-2 receptor erbb-3 receptor flow cytometry gene expression profiling gene expression regulation gene library gene targeting genetic promoter regions genetic transcription green fluorescent proteins histidine human genome humans kidney luminescent proteins lysine mice molecular cloning molecular models molecular sequence data mutation nucleic acid conformation oligonucleotides peptide library pliability polymerase chain reaction protein conformation protein engineering proteomics recombinant proteins reporter genes retroviridae secondary protein structure sequence analysis site-directed mutagenesis substrate specificity tertiary protein structure transcription factors transfection up-regulation x-ray crystallography zinc fingers

iCRTool Content

http://210.212.215.199/icr/index.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Interactions, Pathways, Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

jPREdictorTool Content

http://bibiserv.techfak.uni-bielefeld.de/jpredictor/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.

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tagsanimals binding sites drosophila melanogaster drosophila proteins genomics response elements transcription factors transcriptional regulatory elements

siVirusTool Content

http://sivirus.rnai.jp/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Other Organisms
RNA > Structure Prediction, Visualization, and Design

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.

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tagsanti-hiv agents antiviral agents base sequence conserved sequence genetic variation rna interference rna viruses small interfering rna viral rna

Expression > Networks

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

Expression > Protein Expression

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

Expression > Splicing

ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

QGRS MapperTool Content

http://bioinformatics.ramapo.edu/QGRS/index.php

DNA > Structure and Sequence Feature Detection
Expression > Splicing
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

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tagsdna dna sequence analysis g-quadruplexes guanine oligonucleotides rna rna sequence analysis

RegRNATool Content

http://regrna.mbc.nctu.edu.tw/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Splicing
RNA > Functional RNAs
RNA > Motifs

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

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tagsanimals humans messenger rna mice nucleic acid conformation nucleic acid sequence homology rats ribonucleic acid regulatory sequences rna sequence analysis systems integration untranslated regions

Expression > Transcript Expression Analysis

ACTTool Content

http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php

Expression > Transcript Expression Analysis
Model Organisms > Plants

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

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tagsalgorithms arabidopsis circadian rhythm gene expression profiling oligonucleotide array sequence analysis plant genes transcription factors

BTWTool Content

http://bioinformatics.bc.edu/clotelab/BTW/

Expression > Transcript Expression Analysis

Boltzmann Time Warping (BTW) computes time warping distances and Boltzmann\' pair probabilities for a given input gene expression time series. This tool helps to identify genes that may share similar expression patterns over time.

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tagsalgorithms gene expression profiling genomics humans sequence alignment time factors

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

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tagsbiological models computer simulation gene expression profiling genetic databases genomics oligonucleotide array sequence analysis protein databases protein interaction mapping saccharomyces cerevisiae proteins signal transduction systems biology systems integration

CAPwebTool Content

http://bioinfo.curie.fr/CAPweb/

Expression > Transcript Expression Analysis

CGH array Analysis Platform (CAPweb) is a tool for storing, analyzing and visualizing CGH-array data.

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tagsalgorithms chromosome breakage chromosome mapping computational biology dna dna mutational analysis dna sequence analysis gene dosage genetic models genetic variation genomics humans in situ hybridization oligonucleotide array sequence analysis reproducibility of results sensitivity and specificity statistical models stochastic processes urinary bladder neoplasms

CARMAwebTool Content

https://carmaweb.genome.tugraz.at/carma/

Expression > Transcript Expression Analysis

Comprehensive R based Microarray Analysis web service (CARMAweb) is a resource for the analyses of microarray data including data preprocessing, detection for differentially expressed genes, cluster analysis, and GO analysis. Calculations are performed in R using functions provided by BioConductor.

This content is being maintained by johannes.rainer.

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tagscluster analysis controlled vocabulary gene expression profiling oligonucleotide array sequence analysis

CEASTool Content

http://ceas.cbi.pku.edu.cn

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Cis-regulatory Element Annotation System (CEAS) is a resource for ChIP-chip analyses that retrieves repeat-masked genomic sequences, calculates GC content, plots evolutionary conservation, maps nearby genes, and identifies enriched transcription factor binding (TFBS) motifs.

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tagsbinding sites chromatin immunoprecipitation genomics human genome humans oligonucleotide array sequence analysis transcription factors transcriptional regulatory elements

CMATool Content

http://www.gene-regulation.com/pub/programs/cma/CMA.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

Composite Module Analyst (CMA) defines promoter models based on the composition of transcription factor binding sites (TFBS) in regulatory sequences for sets of coregulated genes.

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tagsalgorithms amino acid sequence binding sites chemical models computer simulation dna sequence analysis endothelial cells gene expression profiling genetic promoter regions humans molecular sequence data protein binding protein sequence analysis transcription factors

CRSDDatabase Content

http://140.120.213.10:8080/crsd/main/home.jsp

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
RNA > Functional RNAs

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

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tags3' untranslated regions binding sites cluster analysis gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics humans micrornas oligonucleotide array sequence analysis transcription factors

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

The Gene Expression Pattern Analysis Suite (GEPAS) is a collection of tools for the analysis of microarray data. GEPAS includes tools for data pre-processing, clustering, differential gene expression, predictors, array CGH and functional annotation. A new pipeline module allows for automation of sequential analysis steps.

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tagsalgorithms cluster analysis drug dose-response relationship gene expression profiling genetic polymorphism kinetics oligonucleotide array sequence analysis systems integration

JProGOTool Content

http://www.jprogo.de/index.jsp

Expression > Transcript Expression Analysis
Model Organisms > Microbes

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

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tagsarchaea archaeal genes bacteria bacterial genes controlled vocabulary gene expression profiling oligonucleotide array sequence analysis statistical data interpretation

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

POXOTool Content

http://www.bioinfo.biocenter.helsinki.fi/poxo

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis

POXO is a series of tools that can be used to discover, search and verify possible regulatory cis-element(s) from set(s) co-expressed genes.

This content is being maintained by mkankain.

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tagsarabidopsis binding sites cluster analysis computational biology dna sequence analysis down-regulation gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics hydrogen peroxide itraconazole oligonucleotide array sequence analysis reproducibility of results software design statistical data interpretation transcription factors transcriptional regulatory elements up-regulation

SNPmaskerTool Content

http://bioinfo.ebc.ee/snpmasker/

DNA > Sequence Polymorphisms
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Expression > Transcript Expression Analysis
Human Genome > Sequence Polymorphisms

SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.

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tagsalleles animals dna primers genomics human genome humans mice nucleic acid databases nucleic acid probes nucleic acid repetitive sequences single nucleotide polymorphism

Expression > cDNA, EST, SAGE

ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

EGassemblerTool Content

http://egassembler.hgc.jp

DNA > Mapping and Assembly
Expression > cDNA, EST, SAGE

EGassembler is a pipeline for clustering and assembling sequence fragments from transcript (EST) data or from shotgun sequencing.

This content is being maintained by amasoudin.

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tagscomputational biology dna sequence analysis expressed sequence tags genomics

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE
Model Organisms > Plants

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

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tagsbase sequence conserved sequence dna primers expressed sequence tags fabaceae genetic markers genetic polymorphism genomics nucleic acid databases poaceae polymerase chain reaction sequence alignment

Human Genome > Annotations

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

TACTTool Content

http://jbirc.jbic.or.jp/tact/

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

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tagsalternative splicing amino acid motifs amino acid sequence base sequence complementary dna computational biology dna sequence analysis expressed sequence tags genes genetic databases genetic models genetic polymorphism genetic transcription human genome humans messenger rna microsatellite repeats molecular sequence data nucleic acid databases open reading frames protein databases proteins rna sequence analysis sequence analysis single nucleotide polymorphism systems integration tertiary protein structure

TavernaTool Content

http://taverna.sourceforge.net/

Computer Related > Web Services
DNA > Annotations
DNA > Gene Prediction
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Taverna is a tool for creating and running bioinformatics workflows.

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tagscomputational biology database management systems genetic databases genomics online systems sequence analysis software design systems integration
setsUniversity of Manchester

WEGOTool Content

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Protein > Annotation and Function

Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram.

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tagscontrolled vocabulary genes genomics

Human Genome > Databases

KOBASTool Content

http://kobas.cbi.pku.edu.cn

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

Human Genome > Health and Disease

DyNAVacSTool Content

http://miracle.igib.res.in/dynavac/

DNA > Tools For the Bench
Human Genome > Health and Disease

DyNAVacS is a tool for designing DNA vaccines that includes steps for chosing a suitable expression vector, ensuring optimal expression by codon optimization, engineering CpG motifs for enhancing immune responses, and providing additional sequence signals for efficient translation. It also allows includes restriction enzyme mapping and design of primers spanning user specified sequences.

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tagscodon computational biology cpg islands dna primers dna vaccines drug design gene expression polymerase chain reaction restriction mapping systems integration

SNP@DomainTool Content

http://snpnavigator.net/

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Domains and Motifs

SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.

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tagshumans protein databases protein sequence analysis single nucleotide polymorphism tertiary protein structure

Human Genome > Other Resources

PrimerStationTool Content

http://ps.cb.k.u-tokyo.ac.jp/

DNA > Tools For the Bench
Human Genome > Other Resources

PrimerStation is a multiplex genomic PCR primer design tool specific for the human genome.

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tagsdna primers genomics human genome humans polymerase chain reaction temperature

SVMHCTool Content

http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/

DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.

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tagsalleles animals artificial intelligence computational biology histocompatibility antigens histocompatibility antigens class i hla antigens humans mice peptides predictive value of tests protein binding protein databases protein sequence analysis sensitivity and specificity single nucleotide polymorphism t-lymphocyte epitopes

TFBSclusterTool Content

http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources
Model Organisms > Mouse and Rat

TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.

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tagsalgorithms animals base sequence binding sites chromosome mapping cluster analysis conserved sequence dna sequence analysis gene expression profiling gene expression regulation genetic promoter regions genetic transcription genomics humans mice molecular sequence data nucleic acid sequence homology protein binding sequence alignment transcription factors transcriptional regulatory elements

Human Genome > Sequence Polymorphisms

FastSNPTool Content

http://fastsnp.ibms.sinica.edu.tw

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

Function Analysis and Selection Tool for Single Nucleotide Polymorphisms (FastSNP) allows users to identify and prioritize SNPs that are likely to have functional effects.

This content is being maintained by fastsnp.

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tagsgene frequency genetic predisposition to disease phenotype proteins risk single nucleotide polymorphism

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

PDATool Content

http://pda.uab.es/pda2/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Sequence Comparison > Analysis of Aligned Sequences

PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.

This content is being maintained by soniacas.

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tagsalgorithms animals dna sequence analysis drosophila genetic polymorphism nucleic acid databases sequence alignment

PupaSuiteTool Content

http://pupasuite.bioinfo.cipf.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

PupaSuite is a SNP analysis tool that allows for the selection of relevant SNPs within a gene based on the characteristics of the SNP. PupaSuite also provides information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs. PupaSuite was created to join PupaSNP & PupasView.

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tagsalgorithms amino acid substitution binding sites genetic transcription genotype haplotypes humans linkage disequilibrium molecular evolution nucleic acid databases phenotype rna splicing single nucleotide polymorphism transcription factors

SNP@DomainTool Content

http://snpnavigator.net/

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Domains and Motifs

SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.

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tagshumans protein databases protein sequence analysis single nucleotide polymorphism tertiary protein structure

SNPmaskerTool Content

http://bioinfo.ebc.ee/snpmasker/

DNA > Sequence Polymorphisms
DNA > Structure and Sequence Feature Detection
DNA > Tools For the Bench
Expression > Transcript Expression Analysis
Human Genome > Sequence Polymorphisms

SNPmasker masks SNPs in a given sequence using information from the dbSNP database. This tool can also be used to mask repeat sequences. SNPmasker is primarily designed for masking the sequences before primer and probe design.

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tagsalleles animals dna primers genomics human genome humans mice nucleic acid databases nucleic acid probes nucleic acid repetitive sequences single nucleotide polymorphism

SVMHCTool Content

http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/

DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.

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tagsalleles animals artificial intelligence computational biology histocompatibility antigens histocompatibility antigens class i hla antigens humans mice peptides predictive value of tests protein binding protein databases protein sequence analysis sensitivity and specificity single nucleotide polymorphism t-lymphocyte epitopes

Literature > Search Tools

HubMedTool Content

http://www.hubmed.org/

Literature > Search Tools

HubMed uses information from PubMed's database, provided by the NCBI through the EUtils web service, to produce a search interface focused on browsing, organising and gathering information from the biomedical literature.

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tagspubmed systems integration

botXminerDatabase Content

http://botdb.abcc.ncifcrf.gov/

Literature > Search Tools
Literature > Text Mining and Semantics

botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either \'botulinum\' or \'tetanus\' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB.

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tagsamino acid sequence botulinum toxins database management systems medline molecular sequence data protein databases tetanus toxin

Literature > Text Mining and Semantics

botXminerDatabase Content

http://botdb.abcc.ncifcrf.gov/

Literature > Search Tools
Literature > Text Mining and Semantics

botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either \'botulinum\' or \'tetanus\' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB.

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tagsamino acid sequence botulinum toxins database management systems medline molecular sequence data protein databases tetanus toxin

Model Organisms > Fly

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

Model Organisms > General Resources

WEGOTool Content

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Protein > Annotation and Function

Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram.

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tagscontrolled vocabulary genes genomics

Model Organisms > Microbes

BAGELDatabase Content

http://bioinformatics.biol.rug.nl/websoftware/bagel/bagel_start.php

DNA > Gene Prediction
Model Organisms > Microbes

BActeriocin GEnome mining tooL (BAGEL) identifies putative bacteriocin ORFs (antimicrobial peptides) based on a database containing information about known bacteriocins and adjacent genes involved in bacteriocin activity.

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tagsamino acid motifs bacterial genome bacteriocins genetic databases genomics multigene family open reading frames

JProGOTool Content

http://www.jprogo.de/index.jsp

Expression > Transcript Expression Analysis
Model Organisms > Microbes

JProGO is a tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information.

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tagsarchaea archaeal genes bacteria bacterial genes controlled vocabulary gene expression profiling oligonucleotide array sequence analysis statistical data interpretation

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

NASTTool Content

http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
RNA > General Resources
Sequence Comparison > Multiple Sequence Alignments

Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

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tagsalgorithms archaeal genes bacillus anthracis bacterial genes cluster analysis computer-aided design dna probes dna sequence analysis equipment design gene expression profiling nucleic acid sequence homology oligonucleotide array sequence analysis ribosomal rna rrna genes sequence alignment staphylococcus aureus

PROFtmbTool Content

http://cubic.bioc.columbia.edu/services/proftmb/

Model Organisms > Microbes
Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes.

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tagsbacterial genome bacterial proteins gram-negative bacteria markov chains membrane proteins protein sequence analysis proteome proteomics reproducibility of results secondary protein structure sequence alignment

TiCoTool Content

http://tico.gobics.de/

DNA > Gene Prediction
Model Organisms > Microbes

TIS Correction (TiCo) is a tool for improving predictions of prokaryotic Translation Initiation Sites (TIS). TiCo can be used to analyze and reannotate predictions obtained by the program GLIMMER.

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tagsalgorithms artificial intelligence automated pattern recognition bacterial genome base sequence cluster analysis dna sequence analysis genomics initiator codon molecular sequence data prokaryotic cells prokaryotic initiation factors protein biosynthesis translational peptide chain initiation

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

jpHMMTool Content

http://jphmm.gobics.de/

Model Organisms > Microbes
Model Organisms > Other Organisms

Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.

This content is being maintained by akschultz.

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tagsalgorithms amino acid sequence homology base sequence dna breaks genetic recombination genomics hiv-1 markov chains phylogeny proteins reproducibility of results sequence alignment tertiary protein structure viral genome

sgTargetTool Content

http://www.ysbl.york.ac.uk/sgTarget/

Model Organisms > Microbes
Protein > 3-D Structure Prediction
Protein > Proteomics

sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties.

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tagsanimals genomics plasmodium falciparum protein conformation protein sequence analysis proteins protozoan proteins

Model Organisms > Mouse and Rat

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

TFBSclusterTool Content

http://hscl.cimr.cam.ac.uk/TFBScluster_genome_portal.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources
Model Organisms > Mouse and Rat

TFBScluster is a web tool designed to identify clusters of transcription factor binding sites (TFBSs) conserved in mammalian and mouse genomes. By entering a specified range of TFBS, you can retrieve a list of SWISS-PROT characterized genes to which the clusters are localized.

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tagsalgorithms animals base sequence binding sites chromosome mapping cluster analysis conserved sequence dna sequence analysis gene expression profiling gene expression regulation genetic promoter regions genetic transcription genomics humans mice molecular sequence data nucleic acid sequence homology protein binding sequence alignment transcription factors transcriptional regulatory elements

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

Model Organisms > Other Organisms

jpHMMTool Content

http://jphmm.gobics.de/

Model Organisms > Microbes
Model Organisms > Other Organisms

Jumping Profile Hidden Markov Model (jpHMM) takes a HIV-1 genome sequence and uses a pre-calculated multiple alignment of the major HIV-1 subtypes to predict the phylogenetic breakpoints and HIV subtype of the submitted sequence.

This content is being maintained by akschultz.

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tagsalgorithms amino acid sequence homology base sequence dna breaks genetic recombination genomics hiv-1 markov chains phylogeny proteins reproducibility of results sequence alignment tertiary protein structure viral genome

siVirusTool Content

http://sivirus.rnai.jp/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Other Organisms
RNA > Structure Prediction, Visualization, and Design

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.

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tagsanti-hiv agents antiviral agents base sequence conserved sequence genetic variation rna interference rna viruses small interfering rna viral rna

Model Organisms > Plants

ACTTool Content

http://www.arabidopsis.leeds.ac.uk/act/coexpanalyser.php

Expression > Transcript Expression Analysis
Model Organisms > Plants

Arabidopsis Co-expression Tool (ACT) is a resource for investigating the co-expression of genes in the NASC/GARNet microarray-based gene expression dataset from Arabidopsis.

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tagsalgorithms arabidopsis circadian rhythm gene expression profiling oligonucleotide array sequence analysis plant genes transcription factors

GeMprospectorTool Content

http://cgi-www.daimi.au.dk/cgi-chili/GeMprospector/main

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE
Model Organisms > Plants

GeMprospector is designed to find cross-species genetic marker candidates in legumes and grasses. GeMprospector automates PCR primer design based on multiple sequence alignments of submitted ESTs and their homologues in sequence databases from legumes or grasses.

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tagsbase sequence conserved sequence dna primers expressed sequence tags fabaceae genetic markers genetic polymorphism genomics nucleic acid databases poaceae polymerase chain reaction sequence alignment

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

Model Organisms > Yeast

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

Other Molecules > Carbohydrates

GlyNest and CASPERTool Content

http://www.glycosciences.de/sweetdb/start.php?action=form_shift_estimation

Other Molecules > Carbohydrates

GlyNest and CASPER are two independent services, available through this common interface, for predicting NMR spectra given a glycan chemical structure.

This content is being maintained by luetteke.

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tagsalgorithms automatic data processing bacterial capsules bacterial polysaccharides biomolecular nuclear magnetic resonance carbohydrate conformation carbohydrate sequence carbohydrates carbon isotopes computational biology computer simulation factual databases forecasting glycopeptides glycoproteins hydrogen magnetic resonance spectroscopy molecular models molecular sequence data molecular structure o antigens oligosaccharides polysaccharides systems integration three-dimensional imaging

Other Molecules > Small Molecules

FAF-DrugsTool Content

http://bioserv.rpbs.jussieu.fr/Help/FAFDrugs.html

Other Molecules > Small Molecules

Free ADME/tox Filtering (FAF-Drugs) allows users to process their own compound collections via simple absorption, distribution, metabolism, excretion and toxicity (ADME/tox) filtering rules to aid in the drug discovery process.

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tagsdrug design drug toxicity pharmaceutical preparations pharmacokinetics

TarFisDockTool Content

http://www.dddc.ac.cn/tarfisdock/

Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets.

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tagsdrug design ligands protein databases proteins tamoxifen vitamin e

Protein > 2-D Structure Prediction

HHrepTool Content

http://toolkit.tuebingen.mpg.de/hhrep

Protein > 2-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).

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tagsamino acid repetitive sequences markov chains protein folding protein sequence analysis sequence alignment

LocalizomeTool Content

http://localodom.kobic.re.kr/LocaloDom/

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.

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tagscell compartmentation eukaryotic cells membrane proteins protein databases reproducibility of results secondary protein structure tertiary protein structure

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

PONGOTool Content

http://pongo.biocomp.unibo.it/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.

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tagsalgorithms artificial intelligence automated pattern recognition humans lipoproteins membrane proteins neural networks (computer) protein conformation protein sequence analysis protein sorting signals reproducibility of results sensitivity and specificity sequence alignment

PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

PROFtmbTool Content

http://cubic.bioc.columbia.edu/services/proftmb/

Model Organisms > Microbes
Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes.

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tagsbacterial genome bacterial proteins gram-negative bacteria markov chains membrane proteins protein sequence analysis proteome proteomics reproducibility of results secondary protein structure sequence alignment

SpritzTool Content

http://distill.ucd.ie/spritz/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

Spritz is a tool for the prediction of disordered regions of proteins.

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tagsalgorithms amino acid sequence artificial intelligence chemical models computer simulation molecular models molecular sequence data protein conformation protein sequence analysis proteins secondary protein structure sequence alignment

transFoldTool Content

http://bioinformatics.bc.edu/clotelab/transFold

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments.

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tagsamino acids bacterial outer membrane proteins membrane proteins secondary protein structure

Protein > 3-D Structural Features

ArchPredTool Content

http://manaslu.aecom.yu.edu/loopred/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.

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tagsalgorithms molecular models protein conformation

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

FeatureMap3DTool Content

http://www.cbs.dtu.dk/services/FeatureMap3D/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology amino acids conserved sequence exons molecular models protein conformation protein databases protein structural homology proteins sequence alignment

HarmonyTool Content

http://caps.ncbs.res.in/harmony/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Sequence Comparison > Analysis of Aligned Sequences

Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.

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tagsalgorithms amino acid substitution amino acids hydrogen bonding molecular models protein conformation protein sequence analysis proteins solvents

KinDOCKTool Content

http://abcis.cbs.cnrs.fr/kindock/

Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).

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tagsadenosine triphosphate binding sites drug design ligands protein conformation protein kinase inhibitors protein kinases

PASTTool Content

http://past.in.tum.de/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amino acids.

This content is being maintained by taeubig.

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tagsprotein conformation protein databases time factors

PDB_HydroTool Content

http://lorentz.immstr.pasteur.fr/solvate_mutate.php

Protein > 3-D Structural Features
Protein > Biochemical Features

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.

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tagsbinding sites dimerization lipids mathematical computing membrane proteins nucleic acids protein conformation protein databases proteins solvents static electricity water

PHEPSTool Content

http://pheps.orgchm.bas.bg/home.html

Protein > 3-D Structural Features
Protein > Biochemical Features

pH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file.

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tagshydrogen-ion concentration ions proteins protons static electricity

PREDITORTool Content

http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.py

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions.

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tagsbiomolecular nuclear magnetic resonance molecular structure proteins torsion abnormality

PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

PreBITool Content

http://pre-s.protein.osaka-u.ac.jp/prebi/

Protein > 3-D Structural Features

Prediction of Biological Interfaces (PreBI) is a server for predicting protein-protein interfaces in protein structures that maximizes both the degree of complementarity and the interface area.

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tagsdatabase management systems humans hydrophobic and hydrophilic interactions molecular models multiprotein complexes protein conformation protein databases proteins static electricity three-dimensional imaging x-ray crystallography

ProKwareTool Content

http://ProKware.mbc.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.

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tagsbinding sites molecular models post-translational protein processing protein databases proteins systems integration tertiary protein structure

ProSAT2Tool Content

http://projects.villa-bosch.de/dbase/ps2/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures

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tagsamino acids chromosome mapping data display molecular structure mutation protein conformation protein databases proteins three-dimensional imaging

ProtemotTool Content

http://protemot.csbb.ntu.edu.tw/

Protein > 3-D Structural Features

The Protein motif (Protemot) server predicts protein binding sites based on structural templates automatically extracted from crystal structures of protein-ligand complexes in the PDB.

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tagsbinding sites ligands molecular models protein databases protein structural homology proteins tertiary protein structure x-ray crystallography

ReadOutTool Content

http://gibk26.bio.kyutech.ac.jp/jouhou/readout/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > 3-D Structural Features

Readout is a server for the calculation of direct and indirect readout energy Z-scores which estimate the degree of sequence specificity of the protein-DNA complex. Readout can be useful for checking the quality of protein-DNA interactions in three dimensional (3D) structures.

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tagsbacterial proteins base sequence binding sites biological models dimerization dna dna primers dna-binding proteins endonucleases gene expression regulation genetic promoter regions glucocorticoid receptors hydrogen bonding macromolecular substances metalloproteins molecular models nucleic acid conformation protein binding protein conformation protein kinases protein subunits proteins repressor proteins saccharomyces cerevisiae proteins tertiary protein structure thermodynamics type ii site-specific deoxyribonucleases viral proteins viral regulatory and accessory proteins water zinc fingers

SWAKKTool Content

http://oxytricha.princeton.edu/SWAKK/

DNA > Phylogeny Reconstruction
Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Sequence Comparison > Pairwise Sequence Alignments

Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.

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tagsamino acid substitution computational biology dna sequence analysis genetic selection protein conformation proteins sequence alignment

Protein > 3-D Structure Comparison

3DSSTool Content

http://cluster.physics.iisc.ernet.in/3dss/options.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary.

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tagsmolecular models phospholipases a protein databases protein structural homology water

OPAASTool Content

http://opaas.ibms.sinica.edu.tw/

Protein > 3-D Structure Comparison

Optimal, Permuted, and Other Alternative Alignments of Protein Structures (OPAAS) is a tool for investigating structural neighbors that can calculate a structural alignment for two protein structures.

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tagsprotein structural homology secondary protein structure

PASTTool Content

http://past.in.tum.de/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison

Polypeptide Angles Suffix Tree (PAST) provides methods for searching three-dimensional protein structures and identifying frequent common substructures (structural motifs) using an approach independent of the sequence of amino acids.

This content is being maintained by taeubig.

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tagsprotein conformation protein databases time factors

PBETool Content

http://bioinformatics.univ-reunion.fr/PBE/

Protein > 3-D Structure Comparison

Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database.

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tagsamino acid motifs artificial intelligence bayes theorem cluster analysis computer simulation factual databases forecasting ligases molecular models neural networks (computer) peptide fragments protein conformation protein databases protein folding protein sequence analysis proteins secondary protein structure sequence alignment ubiquitins

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Protein > 3-D Structure Prediction

(PS)2 Protein Structure Prediction ServerTool Content

http://ps2.life.nctu.edu.tw

Protein > 3-D Structure Prediction

(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.

NAR Web Server Issue 2006
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tagsamino acid sequence consensus sequence molecular models protein conformation protein sequence analysis sequence alignment

ArchPredTool Content

http://manaslu.aecom.yu.edu/loopred/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

ArchPRED predicts the structure of loop regions in protein structures based on a fragment-search based method. Given a query loop of unknown structure, ArchPRED identifies which loops of know structures are likely to share conformational similarity with the query loop.

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tagsalgorithms molecular models protein conformation

CUPSATTool Content

http://cupsat.uni-koeln.de/

Protein > 3-D Structure Prediction
Protein > Biochemical Features

Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.

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tagsmolecular structure point mutation protein databases protein denaturation protein engineering protein folding proteins secondary protein structure solvents

HarmonyTool Content

http://caps.ncbs.res.in/harmony/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Sequence Comparison > Analysis of Aligned Sequences

Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.

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tagsalgorithms amino acid substitution amino acids hydrogen bonding molecular models protein conformation protein sequence analysis proteins solvents

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

PREDITORTool Content

http://wishart.biology.ualberta.ca/shiftor/cgi-bin/preditor_current.py

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction

PREDITOR predicts torsion angles in proteins from NMR chemical shift data and sequence homology. PREDITOR combines sequence alignment methods with advanced chemical shift analysis techniques to generate its torsion angle predictions.

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tagsbiomolecular nuclear magnetic resonance molecular structure proteins torsion abnormality

RosettaDesignTool Content

http://rosettadesign.med.unc.edu

Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography

SABBACTool Content

http://bioserv.rpbs.jussieu.fr/cgi-bin/SABBAC

Protein > 3-D Structure Prediction

Structural Alphabet based protein Backbone Builder from Alpha Carbon trace (SABBAC) is a tool for the reconstruction of complete protein structures from their alpha-carbon descriptions.

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tagscarbon markov chains molecular models peptides protein conformation

SpritzTool Content

http://distill.ucd.ie/spritz/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

Spritz is a tool for the prediction of disordered regions of proteins.

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tagsalgorithms amino acid sequence artificial intelligence chemical models computer simulation molecular models molecular sequence data protein conformation protein sequence analysis proteins secondary protein structure sequence alignment

sgTargetTool Content

http://www.ysbl.york.ac.uk/sgTarget/

Model Organisms > Microbes
Protein > 3-D Structure Prediction
Protein > Proteomics

sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties.

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tagsanimals genomics plasmodium falciparum protein conformation protein sequence analysis proteins protozoan proteins

Protein > 3-D Structure Retrieval/Viewing

3DSSTool Content

http://cluster.physics.iisc.ernet.in/3dss/options.html

Protein > 3-D Structure Comparison
Protein > 3-D Structure Retrieval/Viewing

3-Dimensional Structural Superposition (3DSS) is a tool for superposing two or more protein structures that uses RASMOL for visualization; some browser configuration is necessary.

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tagsmolecular models phospholipases a protein databases protein structural homology water

CASTpTool Content

http://sts.bioengr.uic.edu/castp/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Computed Atlas of Surface Topography of proteins (CASTp) locates and measures concave surface regions on 3D protein structures. This tool can be used to study surface features, binding sites, and functional regions of proteins.

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tagsalgorithms amino acids bacterial proteins bacteriorhodopsins binding sites enzymes ligands macromolecular substances mathematical computing molecular models myoglobin nucleic acid conformation protein conformation protein databases protein sequence analysis proteins ribonucleases sequence alignment single nucleotide polymorphism tertiary protein structure

FISHTool Content

http://max.ucmp.umu.se/sahmm/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.

NAR Web Server Issue 2006
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tagsamino acid sequence homology markov chains protein databases tertiary protein structure

FeatureMap3DTool Content

http://www.cbs.dtu.dk/services/FeatureMap3D/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.

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tagsamino acid sequence amino acid sequence homology amino acids conserved sequence exons molecular models protein conformation protein databases protein structural homology proteins sequence alignment

ProKwareTool Content

http://ProKware.mbc.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.

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tagsbinding sites molecular models post-translational protein processing protein databases proteins systems integration tertiary protein structure

ProSAT2Tool Content

http://projects.villa-bosch.de/dbase/ps2/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing

Protein Structure Annotation Tool (ProSAT2) is a tool for the visualization of sequence based, residue-specific annotations mapped onto three-dimensional (3D) protein structures

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tagsamino acids chromosome mapping data display molecular structure mutation protein conformation protein databases proteins three-dimensional imaging

ReMusTool Content

http://140.121.196.30/remus.asp

Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Features

REinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals antibody specificity cattle chemical models computational biology conserved sequence epitope mapping epitopes humans mice molecular models molecular sequence data monoclonal antibodies pancreatic ribonuclease peptides protein conformation protein sequence analysis proteins sequence alignment structure-activity relationship

SNP@DomainTool Content

http://snpnavigator.net/

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Domains and Motifs

SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.

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tagshumans protein databases protein sequence analysis single nucleotide polymorphism tertiary protein structure

Protein > Annotation and Function

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

SNP@DomainTool Content

http://snpnavigator.net/

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Domains and Motifs

SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.

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tagshumans protein databases protein sequence analysis single nucleotide polymorphism tertiary protein structure

TreeDetTool Content

http://treedetv2.bioinfo.cnio.es/treedet/index.html

Protein > Annotation and Function
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.

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tagsalgorithms amino acid sequence conserved sequence cyclins gtp-binding proteins molecular models molecular sequence data multigene family phylogeny protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins p21(ras) sequence alignment structure-activity relationship tertiary protein structure theoretical models

WEGOTool Content

http://wego.genomics.org.cn/cgi-bin/wego/index.pl

DNA > Annotations
Human Genome > Annotations
Model Organisms > General Resources
Protein > Annotation and Function

Web Gene Ontology Annotation Plot (WEGO) helps visualize the annotation of sets of genes. WEGO can compare gene annotation datasets by plotting the distribution of gene ontology (GO) annotation results into a histogram.

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tagscontrolled vocabulary genes genomics

Protein > Biochemical Features

CUPSATTool Content

http://cupsat.uni-koeln.de/

Protein > 3-D Structure Prediction
Protein > Biochemical Features

Cologne University Protein Stability Analysis Tool (CUPSAT) is a tool to analyse and predict protein stability changes upon point mutations (single amino acid mutations) for known protein structures.

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tagsmolecular structure point mutation protein databases protein denaturation protein engineering protein folding proteins secondary protein structure solvents

DISULFINDTool Content

http://disulfind.dsi.unifi.it/

Protein > Biochemical Features
Protein > Sequence Features

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.

This content is being maintained by paolo.frasconi.

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tagsalgorithms amino acid sequence artificial intelligence binding sites computational biology computer simulation cysteine disulfide bridges disulfides gene expression profiling histidine machine learning metalloproteins molecular evolution molecular sequence data neural networks (computer) protein binding protein databases protein sequence analysis proteins sequence alignment

DiANNATool Content

http://bioinformatics.bc.edu/clotelab/DiANNA/

Protein > Biochemical Features
Protein > Sequence Features

DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.

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tagsalgorithms artificial intelligence binding sites chemical models computer simulation cysteine disulfides neural networks (computer) oxidation-reduction protein binding protein conformation protein interaction mapping protein sequence analysis proteins secondary protein structure sequence alignment structure-activity relationship

MODiTool Content

http://prix.uos.ac.kr/research.jsp

Protein > Biochemical Features
Protein > Proteomics

Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.

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tagsmass spectrometry peptides post-translational protein processing protein databases protein sequence analysis

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

NAR Web Server Issue 2006
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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

PDB_HydroTool Content

http://lorentz.immstr.pasteur.fr/solvate_mutate.php

Protein > 3-D Structural Features
Protein > Biochemical Features

PDB_Hydro provides tools for mutating and solvating structures of biological macromolecules like proteins or DNA. It identifies strongly and poorly solvated exposed surfaces of structures in an effort to help identify potential interaction zones.

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tagsbinding sites dimerization lipids mathematical computing membrane proteins nucleic acids protein conformation protein databases proteins solvents static electricity water

PHEPSTool Content

http://pheps.orgchm.bas.bg/home.html

Protein > 3-D Structural Features
Protein > Biochemical Features

pH-dependent Protein Electrostatics Server (PHEPS) performs global and local pH-dependent electrostatic analysis of protein structures. The user can supply a PDB ID or upload a coordinate file.

NAR Web Server Issue 2006
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tagshydrogen-ion concentration ions proteins protons static electricity

PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

RosettaDesignTool Content

http://rosettadesign.med.unc.edu

Protein > 3-D Structure Prediction
Protein > Biochemical Features

RosettaDesign identifies low energy sequences for specified protein three dimensional (3D) structures and can been used to predict stable side chain conformations.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence amino acid sequence homology bacterial proteins biomolecular nuclear magnetic resonance circular dichroism computational biology computer simulation crystallization dimerization dna-binding proteins guanidine kinetics magnetic resonance spectroscopy molecular models molecular sequence data monte carlo method mutagenesis mutation protein conformation protein databases protein denaturation protein engineering protein folding protein sequence analysis proteins secondary protein structure sequence alignment solubility temperature tertiary protein structure thermodynamics x-ray crystallography

Protein > Do-it-all Tools for Protein

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

NAR Web Server Issue 2006
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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

Protein > Domains and Motifs

AUGUSTUSTool Content

http://bioinf.uni-greifswald.de/augustus

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Splicing
Protein > Domains and Motifs

AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface, or downloaded and run locally.

This content is being maintained by Mario Stanke.

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tagsadult algorithms alternative splicing animals artificial intelligence automated pattern recognition base sequence bile acids and salts cholic acids chromosome mapping computer simulation deoxycholic acid dna sequence analysis drosophila melanogaster exons female gene components gene expression genes genetic databases genetic models genetic variation genomics human genome humans hypercholesterolemia hyperlipidemias introns ldl lipoproteins male markov chains middle aged molecular sequence data proteins sequence alignment statistical models stochastic processes triglycerides vldl lipoproteins

AlgPredTool Content

http://www.imtech.res.in/raghava/algpred/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.

This content is being maintained by raghavagps.

NAR Web Server Issue 2006
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tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

BindNTool Content

http://bioinformatics.ksu.edu/bindn/

Protein > Domains and Motifs
Protein > Sequence Features

BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).

NAR Web Server Issue 2006
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tagsamino acids artificial intelligence binding sites dna dna-binding proteins molecular models protein sequence analysis rna-binding proteins

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

DILIMOTTool Content

http://dilimot.embl.de/

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.

NAR Web Server Issue 2006
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tagsamino acid motifs amino acid sequence animals binding sites genome humans microtubule-associated proteins molecular models molecular sequence data peptides protein binding protein kinases protein sequence analysis protein sorting signals proteins tertiary protein structure

DOUTfinderDatabase Content

http://mendel.imp.ac.at/dout/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences.

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tagsamino acid sequence homology humans tertiary protein structure

FISHTool Content

http://max.ucmp.umu.se/sahmm/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.

NAR Web Server Issue 2006
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tagsamino acid sequence homology markov chains protein databases tertiary protein structure

LocalizomeTool Content

http://localodom.kobic.re.kr/LocaloDom/

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.

NAR Web Server Issue 2006
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tagscell compartmentation eukaryotic cells membrane proteins protein databases reproducibility of results secondary protein structure tertiary protein structure

MAGIIC-PROTool Content

http://biominer.bime.ntu.edu.tw/magiicpro/

Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented.

NAR Web Server Issue 2006
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tagsbinding sites ligands molecular models multiprotein complexes protein conformation protein sequence analysis

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

NAR Web Server Issue 2006
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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

ProKwareTool Content

http://ProKware.mbc.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs

ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.

NAR Web Server Issue 2006
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tagsbinding sites molecular models post-translational protein processing protein databases proteins systems integration tertiary protein structure

SNP@DomainTool Content

http://snpnavigator.net/

DNA > Sequence Polymorphisms
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Domains and Motifs

SNP@Domain identifies SNPs within human protein domains allowing users to investigate SNPs in the context of two dimensional and three dimensional maps. Links to external databases (Pfam, SCOP, Ensembl, dbSNP, OMIM, SIFT) are also presented.

NAR Web Server Issue 2006
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tagshumans protein databases protein sequence analysis single nucleotide polymorphism tertiary protein structure

SUMOspTool Content

http://sumosp.biocuckoo.org/

Protein > Domains and Motifs

SUMOylation Sites Prediction (SUMOsp) predicts sites for sumoylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO).

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tagsalgorithms computational biology post-translational protein processing proteins small ubiquitin-related modifier proteins

ScanPrositeTool Content

http://prosite.expasy.org/scanprosite/

Protein > Domains and Motifs

ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs.

This content is being maintained by PROSITE.

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tagsamino acid sequence homology amino acids computational biology gene expression profiling protein databases protein sequence analysis proteins sequence alignment tertiary protein structure

TACTTool Content

http://jbirc.jbic.or.jp/tact/

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

NAR Web Server Issue 2006
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tagsalternative splicing amino acid motifs amino acid sequence base sequence complementary dna computational biology dna sequence analysis expressed sequence tags genes genetic databases genetic models genetic polymorphism genetic transcription human genome humans messenger rna microsatellite repeats molecular sequence data nucleic acid databases open reading frames protein databases proteins rna sequence analysis sequence analysis single nucleotide polymorphism systems integration tertiary protein structure

TreeDetTool Content

http://treedetv2.bioinfo.cnio.es/treedet/index.html

Protein > Annotation and Function
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence conserved sequence cyclins gtp-binding proteins molecular models molecular sequence data multigene family phylogeny protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins p21(ras) sequence alignment structure-activity relationship tertiary protein structure theoretical models

TreeDomViewerTool Content

http://www.bioinformatics.nl/tools/treedom

DNA > Phylogeny Reconstruction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

TreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment.

NAR Web Server Issue 2006
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tagsphylogeny protein sequence analysis proteins sequence alignment software design tertiary protein structure

Protein > Interactions, Pathways, Enzymes

APIDTool Content

http://bioinfow.dep.usal.es/apid/

Protein > Interactions, Pathways, Enzymes

Agile Protein Interaction DataAnalyzer (APID) allows you to query protein-protein interactions using a common platform facilitating comparison across different datasets. Currently supported interaction databases are BIND, HPRD, DIP, IntAct, and MINT.

NAR Web Server Issue 2006
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tagscomputational biology protein databases protein interaction mapping

BabelomicsTool Content

http://www.babelomics.org

DNA > Annotations
Expression > Gene Regulation
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes

Babelomics is a suite of web tools for the functional annotation and analysis of groups of genes in high throughput experiments. Tools include: FatiGO, FatiGOplus, Fatiscan, Gene Set Enrichment Analysis (GSEA), Marmite, and the Tissues Mining Tool (TMT). Other tools include Biocarta pathways, Transfac and a tool de novo functional annotation of sequences.

This content is being maintained by juan_aguilar.

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tagsalgorithms animals artificial intelligence binding sites chromosome mapping dna sequence analysis gene expression profiling genes genetic databases genomics humans mice oligonucleotide array sequence analysis phylogeny proteomics rats sequence alignment systems biology systems integration transcription factors

BiologicalNetworksTool Content

http://brak.sdsc.edu/pub/BiologicalNetworks/

Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

BiologicalNetworks allows retrieval, construction, and visualization of biological networks and allows for the analysis of high-throughput expression data by mapping onto network graphs. BiologicalNetworks queries the PathSys system, a combined database of biological pathways, gene regulatory networks, and protein interaction maps.

NAR Web Server Issue 2006
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tagsbiological models computer simulation gene expression profiling genetic databases genomics oligonucleotide array sequence analysis protein databases protein interaction mapping saccharomyces cerevisiae proteins signal transduction systems biology systems integration

DILIMOTTool Content

http://dilimot.embl.de/

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.

NAR Web Server Issue 2006
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tagsamino acid motifs amino acid sequence animals binding sites genome humans microtubule-associated proteins molecular models molecular sequence data peptides protein binding protein kinases protein sequence analysis protein sorting signals proteins tertiary protein structure

KOBASTool Content

http://kobas.cbi.pku.edu.cn

DNA > Annotations
Human Genome > Databases
Protein > Interactions, Pathways, Enzymes

KEGG Orthology-Based Annotation System (KOBAS) annotates sequences with KEGG Orthology terms and identifies the frequently occurring (or significantly enriched) pathways among the queried sequences compared against a background distribution. 5 pathway databases are used (KEGG Pathway, PID, BioCyc, Reactome, Panther) and 5 human databases (OMIM, KEGG Disease, FunDO, GAD, NHGRI GWAS).

NAR Web Server Issue 2006NAR Web Server Issue 2011
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tagsalzheimer disease artificial intelligence biological models chromosome mapping controlled vocabulary database management systems documentation genes genetic databases hippocampus natural language processing proteins proteome sequence analysis signal transduction statistical data interpretation up-regulation

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

PANTHER ToolsTool Content

http://www.pantherdb.org/tools/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis
Human Genome > Annotations
Human Genome > Sequence Polymorphisms
Model Organisms > Fly
Model Organisms > Mouse and Rat
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function. The PANTHER research tools allow you to score proteins against the PANTHER HMM library, use PANTHER to do gene expression analyses, and download PANTHER tools and data.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence animals biological evolution computational biology database management systems gene expression profiling genetic variation humans inborn genetic diseases markov chains mice missense mutation peptide library phylogeny predictive value of tests protein databases protein sequence analysis proteins rats sequence alignment signal transduction single nucleotide polymorphism systems integration terminology as topic tertiary protein structure

SVMHCTool Content

http://www-abi.informatik.uni-tuebingen.de/Services/SVMHC/

DNA > Sequence Polymorphisms
Human Genome > Other Resources
Human Genome > Sequence Polymorphisms
Protein > Interactions, Pathways, Enzymes

SVMHC is a server for prediction of MHC class I and class II binding peptides. SVMHC can be used to find likely binders in a protein sequence and to investigate the effects of single nucleotide polymorphisms on MHC-peptide binding.

NAR Web Server Issue 2006
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tagsalleles animals artificial intelligence computational biology histocompatibility antigens histocompatibility antigens class i hla antigens humans mice peptides predictive value of tests protein binding protein databases protein sequence analysis sensitivity and specificity single nucleotide polymorphism t-lymphocyte epitopes

TavernaTool Content

http://taverna.sourceforge.net/

Computer Related > Web Services
DNA > Annotations
DNA > Gene Prediction
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Taverna is a tool for creating and running bioinformatics workflows.

NAR Web Server Issue 2006
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tagscomputational biology database management systems genetic databases genomics online systems sequence analysis software design systems integration
setsUniversity of Manchester

iCRTool Content

http://210.212.215.199/icr/index.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Interactions, Pathways, Enzymes

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.

NAR Web Server Issue 2006
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tags5' flanking region bacterial genome bacterial proteins binding sites dna-binding proteins genomics mycobacterium tuberculosis nucleic acid regulatory sequences operon prokaryotic cells regulon sequence alignment serine endopeptidases transcription factors transcriptional regulatory elements

metaSHARKTool Content

http://bioinformatics.leeds.ac.uk/shark/

Protein > Interactions, Pathways, Enzymes

Metabolic Search And Reconstruction Kit (metaSHARK) provides an interactive visualisation platform for the KEGG metabolic network in the form of the SHARKview applet.

NAR Web Server Issue 2006
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tagsanimals biological models coenzyme a dna sequence analysis eimeria tenella enzymes gene expression profiling genomics metabolism plasmodium falciparum protozoan genome

Protein > Localization and Targeting

LocalizomeTool Content

http://localodom.kobic.re.kr/LocaloDom/

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting

Localizome predicts transmembrane (TM) helix number and topology for eukaryotic proteins using protein domain information.

NAR Web Server Issue 2006
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tagscell compartmentation eukaryotic cells membrane proteins protein databases reproducibility of results secondary protein structure tertiary protein structure

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

NAR Web Server Issue 2006
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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

PONGOTool Content

http://pongo.biocomp.unibo.it/

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PONGO allows users to compare topology predictions of membrane proteins made by four different predictors (MEMSAT, TMHMM, ENSEMBLE, and PRODIV). It also displays a signal peptide prediction determined with SPEP.

NAR Web Server Issue 2006
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tagsalgorithms artificial intelligence automated pattern recognition humans lipoproteins membrane proteins neural networks (computer) protein conformation protein sequence analysis protein sorting signals reproducibility of results sensitivity and specificity sequence alignment

PROFtmbTool Content

http://cubic.bioc.columbia.edu/services/proftmb/

Model Organisms > Microbes
Protein > 2-D Structure Prediction
Protein > Localization and Targeting

PROFtmb predicts transmembrane beta-barrel (TMB) proteins in Gram-negative bacteria. In addition to running your own predictions, you can also download predictions for all proteins in 78 Gram-Negative bacterial genomes.

NAR Web Server Issue 2006
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tagsbacterial genome bacterial proteins gram-negative bacteria markov chains membrane proteins protein sequence analysis proteome proteomics reproducibility of results secondary protein structure sequence alignment

pTARGETTool Content

http://bioinformatics.albany.edu/~ptarget

Protein > Localization and Targeting

pTARGET predicts the subcellular localization of eukaryotic proteins based on the occurrence patterns of location-specific protein functional domains and the amino acid compositional differences in proteins from nine distinct subcellular locations.

NAR Web Server Issue 2006
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tagsalgorithms amino acid sequence animals eukaryotic cells humans mice molecular sequence data protein sequence analysis proteins proteome proteomics sequence alignment structure-activity relationship subcellular fractions

transFoldTool Content

http://bioinformatics.bc.edu/clotelab/transFold

Protein > 2-D Structure Prediction
Protein > Localization and Targeting

transFold predicts the super-secondary structure of transmembrane beta-barrel (TMB) proteins including side-chain orientation and topology of transmembrane segments.

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tagsamino acids bacterial outer membrane proteins membrane proteins secondary protein structure

Protein > Molecular Dynamics and Docking

FOLD-RATETool Content

http://psfs.cbrc.jp/fold-rate/

Protein > Molecular Dynamics and Docking

FOLD-RATE predicts the folding rates of proteins from their amino acid sequences.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acids binding sites chemical models kinetics linear models molecular models mutation protein conformation protein folding protein sequence analysis protein structural homology proteins secondary protein structure solvents statistical models statistics as topic tertiary protein structure thermodynamics

GRAMM-XTool Content

http://vakser.bioinformatics.ku.edu/resources/gramm/grammx

Protein > Molecular Dynamics and Docking

GRAMM-X is a protein docking server.

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tagsalgorithms antigen-antibody complex automation binding sites computational biology computer simulation dimerization evaluation studies as topic influenza virus hemagglutinin glycoproteins ligands macromolecular substances molecular conformation molecular models multiprotein complexes protein conformation protein databases protein folding protein interaction mapping protein structural homology proteomics reproducibility of results statistical models tertiary protein structure viral antibodies

KinDOCKTool Content

http://abcis.cbs.cnrs.fr/kindock/

Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

KinDOCK is a tool for the analysis of ATP-binding sites of protein kinases based on a structural library of protein kinase-ligand complexes extracted from the Protein Data Bank (PDB).

NAR Web Server Issue 2006
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tagsadenosine triphosphate binding sites drug design ligands protein conformation protein kinase inhibitors protein kinases

NOMAD-RefTool Content

http://lorentz.immstr.pasteur.fr/nomad-ref.php

Protein > Molecular Dynamics and Docking

Normal Mode Analysis, Deformation, and Refinement (NOMAD-Ref) provides tools for calculating functionally relevant movements in biological macromolecules. This resource provides tools for investigating different conformations of large protein structures, for modeling receptor/ligand docking complexes, and for calculating the associated molecular motions.

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tagscarrier proteins computer simulation dna dna-binding proteins dna-directed dna polymerase dna-directed rna polymerases escherichia coli proteins ligands macromolecular substances mathematical computing molecular models molecular structure motion neural networks (computer) protein conformation proteins x-ray diffraction

TarFisDockTool Content

http://www.dddc.ac.cn/tarfisdock/

Other Molecules > Small Molecules
Protein > Molecular Dynamics and Docking

Target Fishing Dock (TarFisDock) is a web server that docks small molecules with protein structures in the Potential Drug Target Database (PDTD) in an effort to discover new drug targets.

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tagsdrug design ligands protein databases proteins tamoxifen vitamin e

oGNMTool Content

http://ignm.ccbb.pitt.edu/GNM_Online_Calculation.htm

Protein > Molecular Dynamics and Docking

Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.

NAR Web Server Issue 2006
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tagsalgorithms binding sites chemical models computational biology computer simulation molecular models molecular structure motion normal distribution nucleic acid conformation oligonucleotides protein binding protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship thermodynamics x-ray crystallography

Protein > Phylogeny Reconstruction

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

PAL2NALTool Content

http://coot.embl.de/pal2nal/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.

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tagscodon dna sequence analysis exons protein sequence analysis sequence alignment

SWAKKTool Content

http://oxytricha.princeton.edu/SWAKK/

DNA > Phylogeny Reconstruction
Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Sequence Comparison > Pairwise Sequence Alignments

Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.

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tagsamino acid substitution computational biology dna sequence analysis genetic selection protein conformation proteins sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

TreeDomViewerTool Content

http://www.bioinformatics.nl/tools/treedom

DNA > Phylogeny Reconstruction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

TreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment.

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tagsphylogeny protein sequence analysis proteins sequence alignment software design tertiary protein structure

Protein > Presentation and Format

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Protein > Proteomics

MODiTool Content

http://prix.uos.ac.kr/research.jsp

Protein > Biochemical Features
Protein > Proteomics

Modi is a tool that facilitates the interpretation of tandem mass spectra in order to identify post-translational modifications (PTMs) in a peptide.

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tagsmass spectrometry peptides post-translational protein processing protein databases protein sequence analysis

NeuropredTool Content

http://neuroproteomics.scs.uiuc.edu/neuropred.html

Protein > Proteomics
Protein > Sequence Features

NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.

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tagsamino acid sequence animals aplysia invertebrate hormones logistic models mass spectrometry neuropeptides protein precursors protein sequence analysis regression analysis sensitivity and specificity statistical models

sgTargetTool Content

http://www.ysbl.york.ac.uk/sgTarget/

Model Organisms > Microbes
Protein > 3-D Structure Prediction
Protein > Proteomics

sgTarget is a structural genomics resource that helps to select and prioritize good targets for structure determination from a list of sequences. Target selection is based on multiple factors including homology searches and a range of physiochemical properties.

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tagsanimals genomics plasmodium falciparum protein conformation protein sequence analysis proteins protozoan proteins

Protein > Sequence Features

BindNTool Content

http://bioinformatics.ksu.edu/bindn/

Protein > Domains and Motifs
Protein > Sequence Features

BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).

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tagsamino acids artificial intelligence binding sites dna dna-binding proteins molecular models protein sequence analysis rna-binding proteins

DISULFINDTool Content

http://disulfind.dsi.unifi.it/

Protein > Biochemical Features
Protein > Sequence Features

DISULFIND is a server for predicting the disulfide bonding state of cysteines and their disulfide connectivity given a protein sequence.

This content is being maintained by paolo.frasconi.

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tagsalgorithms amino acid sequence artificial intelligence binding sites computational biology computer simulation cysteine disulfide bridges disulfides gene expression profiling histidine machine learning metalloproteins molecular evolution molecular sequence data neural networks (computer) protein binding protein databases protein sequence analysis proteins sequence alignment

DiANNATool Content

http://bioinformatics.bc.edu/clotelab/DiANNA/

Protein > Biochemical Features
Protein > Sequence Features

DiANNA (DiAminoacid Neural Network Application) a tool that predicts cysteine states of a protein. It can predict whether a particular cysteine is reduced, is forming a disulfide bond, or is bound to a metallic ligand.

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tagsalgorithms artificial intelligence binding sites chemical models computer simulation cysteine disulfides neural networks (computer) oxidation-reduction protein binding protein conformation protein interaction mapping protein sequence analysis proteins secondary protein structure sequence alignment structure-activity relationship

HHrepTool Content

http://toolkit.tuebingen.mpg.de/hhrep

Protein > 2-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).

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tagsamino acid repetitive sequences markov chains protein folding protein sequence analysis sequence alignment

MAGIIC-PROTool Content

http://biominer.bime.ntu.edu.tw/magiicpro/

Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented.

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tagsbinding sites ligands molecular models multiprotein complexes protein conformation protein sequence analysis

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MeMoTool Content

http://www.bioinfo.tsinghua.edu.cn/%7Etigerchen/memo.html

Protein > Sequence Features

Methylation Modification Prediction Server (MeMo) is a server that predicts arginine and lysine sites that undergo methylation using a support vector machine (SVM).

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tagsarginine artificial intelligence lysine methylation post-translational protein processing proteins

NeuropredTool Content

http://neuroproteomics.scs.uiuc.edu/neuropred.html

Protein > Proteomics
Protein > Sequence Features

NeuroPred is a tool designed to predict cleavage sites at basic amino acid locations in neuropeptide precursor sequences. Neuropred also computes the mass of the predicted peptides with or without selected post-translational modifications.

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tagsamino acid sequence animals aplysia invertebrate hormones logistic models mass spectrometry neuropeptides protein precursors protein sequence analysis regression analysis sensitivity and specificity statistical models

PROFEATTool Content

http://jing.cz3.nus.edu.sg/cgi-bin/prof/prof.cgi

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Sequence Features

Protein Features (PROFEAT) is a tool for computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence. New functions include computation of protein-protein and protein-small molecule interactions, topological descriptors for peptide sequences and small molecule structures. New feature groups of descriptors have also been added.

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tagsalgorithms amino acids computational biology peptides protein conformation protein databases protein sequence analysis proteins

ReMusTool Content

http://140.121.196.30/remus.asp

Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Features

REinforced Merging techniques for Unique peptide Segments (ReMus) is designed for identification of the locations and compositions of unique peptide segments from a set of protein family sequences.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals antibody specificity cattle chemical models computational biology conserved sequence epitope mapping epitopes humans mice molecular models molecular sequence data monoclonal antibodies pancreatic ribonuclease peptides protein conformation protein sequence analysis proteins sequence alignment structure-activity relationship

Protein > Sequence Retrieval

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

RNA > Functional RNAs

CRSDDatabase Content

http://140.120.213.10:8080/crsd/main/home.jsp

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
RNA > Functional RNAs

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).

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tags3' untranslated regions binding sites cluster analysis gene expression profiling gene expression regulation genetic databases genetic promoter regions genomics humans micrornas oligonucleotide array sequence analysis transcription factors

CrossLinkTool Content

http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.ht...

RNA > Functional RNAs
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

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tagsmicrornas rna sequence analysis sequence alignment

RNAhybridTool Content

http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/

Expression > Gene Regulation
RNA > Functional RNAs

RNAhybrid is a tool for predicting miRNA (microRNA) targets by calculating the minimum free energy of hybridization between target RNA and miRNA sequences.

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tags3' untranslated regions algorithms animals binding sites body patterning caenorhabditis elegans caenorhabditis elegans proteins computational biology drosophila homeodomain proteins insect genes messenger rna micrornas nucleic acid conformation nucleic acid databases post-transcriptional rna processing rna interference thermodynamics

RegRNATool Content

http://regrna.mbc.nctu.edu.tw/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Splicing
RNA > Functional RNAs
RNA > Motifs

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

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tagsanimals humans messenger rna mice nucleic acid conformation nucleic acid sequence homology rats ribonucleic acid regulatory sequences rna sequence analysis systems integration untranslated regions

RNA > General Resources

NASTTool Content

http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
RNA > General Resources
Sequence Comparison > Multiple Sequence Alignments

Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

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tagsalgorithms archaeal genes bacillus anthracis bacterial genes cluster analysis computer-aided design dna probes dna sequence analysis equipment design gene expression profiling nucleic acid sequence homology oligonucleotide array sequence analysis ribosomal rna rrna genes sequence alignment staphylococcus aureus

RNA > Motifs

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

MoD ToolsTool Content

http://159.149.109.16/modtools/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs

Tools for Motif Discovery (MoD) in nucleotide sequences that includes: Weeder, a program for detecting transcription factor binding sites (TFBS) in coregulated genes; WeederH, a tool for detecting TFBS and regulatory regions from homologous genes; and RNA profile, a tool for secondary structure motif discovery in RNA sequences.

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tagsbinding sites dna sequence analysis gene expression regulation nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna sequence analysis transcription factors transcriptional regulatory elements untranslated rna

QGRS MapperTool Content

http://bioinformatics.ramapo.edu/QGRS/index.php

DNA > Structure and Sequence Feature Detection
Expression > Splicing
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

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tagsdna dna sequence analysis g-quadruplexes guanine oligonucleotides rna rna sequence analysis

QuadFinderTool Content

http://miracle.igib.res.in/quadfinder/

DNA > Structure and Sequence Feature Detection
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences.

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tagsdna dna sequence analysis g-quadruplexes guanine rna rna sequence analysis

RNAMSTTool Content

http://bioinfo.csie.ncu.edu.tw/~rnamst/

RNA > Motifs

RNA Motif Search Tool (RNAMST) is a tool for identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences.

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tagsnucleic acid conformation rna rna sequence analysis

RegRNATool Content

http://regrna.mbc.nctu.edu.tw/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Splicing
RNA > Functional RNAs
RNA > Motifs

Regulatory RNA (RegRNA) is a server for identifying regulatory RNA motifs and elements in mRNA sequences including: motifs located in the 5\'-UTR and 3\'-UTR; motifs involved in mRNA splicing and transcriptional regulation; other motifs in mRNA such as riboswitches and splice donor/acceptor sites; RNA structural features; and miRNA target sites.

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tagsanimals humans messenger rna mice nucleic acid conformation nucleic acid sequence homology rats ribonucleic acid regulatory sequences rna sequence analysis systems integration untranslated regions

RNA > Sequence Retrieval

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

RNA > Structure Prediction, Visualization, and Design

ARTSTool Content

http://bioinfo3d.cs.tau.ac.il/ARTS/

RNA > Structure Prediction, Visualization, and Design

Alignment of RNA Tertiary Structures (ARTS) is a method for aligning two nucleic acid structures (RNAs or DNAs) and detecting a-priori unknown common substructures.

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tagsalgorithms base sequence chemical models computer simulation molecular models molecular sequence data nucleic acid conformation rna rna sequence analysis sequence alignment untranslated rna

CorreLogoTool Content

http://correlogo.abcc.ncifcrf.gov/

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.

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tagsdna sequence analysis nucleic acid conformation ribosomal rna rna sequence analysis sequence alignment transfer rna

ITS2Tool Content

http://its2.bioapps.biozentrum.uni-wuerzburg.de/

DNA > Phylogeny Reconstruction
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

The Internal Transcribed Spacer 2 Database (ITS2) includes a homology based RNA structure prediction algorithm which allows the detection and secondary structure prediction of ITS2 sequences. This resource also contains more than 25,000 pre-calculated secondary structures for currently known ITS2 sequences that can be searched and browsed via taxonomy.

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tagsanimals base sequence computational biology conserved sequence eukaryota fungal genome fungi genetic databases genetic markers genetic transcription invertebrates molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny plant genome plants ribosomal rna ribosomal spacer dna rna sequence analysis sequence alignment tertiary protein structure

PSEUDOVIEWERTool Content

http://pseudoviewer.inha.ac.kr/

RNA > Structure Prediction, Visualization, and Design

PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.

This content is being maintained by khan.

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tagsalgorithms base pairing base sequence computational biology molecular models molecular sequence data nucleic acid conformation programming languages rna rna sequence analysis

QGRS MapperTool Content

http://bioinformatics.ramapo.edu/QGRS/index.php

DNA > Structure and Sequence Feature Detection
Expression > Splicing
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

Quadruplex forming G-Rich Sequences (QGRS) Mapper searches nucleotide sequences for the presence of G-quartet motifs. QGRS Mapper allows you to view the distribution and composition of QGRS in the context of alternatively spliced isoforms of your gene.

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tagsdna dna sequence analysis g-quadruplexes guanine oligonucleotides rna rna sequence analysis

QuadFinderTool Content

http://miracle.igib.res.in/quadfinder/

DNA > Structure and Sequence Feature Detection
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

QuadFinder is a tool for the identification and analysis of quadruplex forming nucleotide sequences.

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tagsdna dna sequence analysis g-quadruplexes guanine rna rna sequence analysis

siVirusTool Content

http://sivirus.rnai.jp/

DNA > Tools For the Bench
Expression > Gene Regulation
Model Organisms > Other Organisms
RNA > Structure Prediction, Visualization, and Design

siVirus aids in the design of short interfering RNA (siRNA) and helps to identify conserved target sequences for antiviral RNA interference.

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tagsanti-hiv agents antiviral agents base sequence conserved sequence genetic variation rna interference rna viruses small interfering rna viral rna

Sequence Comparison > Alignment Editing and Visualization

Kalign, Kalignvu, and MumsaTool Content

http://msa.cgb.ki.se/cgi-bin/msa.cgi

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality.

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tagsalgorithms dna sequence analysis genome genomics nucleic acid databases protein databases protein sequence analysis reproducibility of results roc curve sequence alignment

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Sequence Comparison > Analysis of Aligned Sequences

CorreLogoTool Content

http://correlogo.abcc.ncifcrf.gov/

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

CorreLogo generates a 3D sequence logo for RNA or DNA alignments. The first two dimensions of the sequence logo display information about the information content and residue composition of individual columns of the alignment. The 3D sequence logo consists of a square matrix that shows columns with high mutual information, a measure of how much the residues in two alignment columns are correlated.

NAR Web Server Issue 2006
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tagsdna sequence analysis nucleic acid conformation ribosomal rna rna sequence analysis sequence alignment transfer rna

FeatureMap3DTool Content

http://www.cbs.dtu.dk/services/FeatureMap3D/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.

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tagsamino acid sequence amino acid sequence homology amino acids conserved sequence exons molecular models protein conformation protein databases protein structural homology proteins sequence alignment

HarmonyTool Content

http://caps.ncbs.res.in/harmony/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Sequence Comparison > Analysis of Aligned Sequences

Harmony is a server to assess the compatibility of an amino acid sequence with a proposed three-dimensional structure.

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tagsalgorithms amino acid substitution amino acids hydrogen bonding molecular models protein conformation protein sequence analysis proteins solvents

Kalign, Kalignvu, and MumsaTool Content

http://msa.cgb.ki.se/cgi-bin/msa.cgi

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality.

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tagsalgorithms dna sequence analysis genome genomics nucleic acid databases protein databases protein sequence analysis reproducibility of results roc curve sequence alignment

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

PAL2NALTool Content

http://coot.embl.de/pal2nal/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.

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tagscodon dna sequence analysis exons protein sequence analysis sequence alignment

PDATool Content

http://pda.uab.es/pda2/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Sequence Comparison > Analysis of Aligned Sequences

PDA (Pipeline Diversity Analysis) is a server which searches for polymorphic sequences in large databases, and estimates their genetic diversity. Results contain sequence alignments (generated by ClustalW) and include statistics on polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for your alignment. The full results set is also available for download as a MySQL database.

This content is being maintained by soniacas.

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tagsalgorithms animals dna sequence analysis drosophila genetic polymorphism nucleic acid databases sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

TreeDetTool Content

http://treedetv2.bioinfo.cnio.es/treedet/index.html

Protein > Annotation and Function
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.

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tagsalgorithms amino acid sequence conserved sequence cyclins gtp-binding proteins molecular models molecular sequence data multigene family phylogeny protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins p21(ras) sequence alignment structure-activity relationship tertiary protein structure theoretical models

Sequence Comparison > Comparative Genomics

MEME SuiteTool Content

http://meme.nbcr.net/meme/intro.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Comparative Genomics

The MEME Suite web server is a unified portal for discovery and analysis of sequence motifs (e.g. DNA binding sites, protein interaction domains). Motifs with/without gaps may be discovered, searched for in DNA and protein databases, compared to other motifs and analyzed for putative function by association with gene ontology terms. MEME is a tool designed for discovering and searching for DNA motifs such as transcription factor binding sites (TFBS) or protein domains.

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tagsalcohol dehydrogenase alcohol oxidoreductases algorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence automated pattern recognition automation bacterial proteins base sequence binding sites biopolymers chemical models consensus sequence dna dna sequence analysis entropy evaluation studies as topic factual databases ferredoxins genetic databases humans hydroxysteroid dehydrogenases mammals markov chains mathematical computing molecular models molecular sequence data nucleic acid repetitive sequences nucleic acid sequence homology oxidoreductases phylogeny protein sequence analysis proteins reproducibility of results secondary protein structure sequence alignment sequence analysis software design stochastic processes streptomyces tertiary protein structure theoretical models transcription factors transcriptional regulatory elements

MicroFootPrinterTool Content

http://bio.cs.washington.edu/MicroFootPrinter.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MicroFootPrinter identifies the conserved motifs in regulatory regions of prokaryotic genomes using the phylogenetic footprinting program FootPrinter.

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tagsalgorithms amino acid sequence homology animals archaeal genome bacterial genome computational biology conserved sequence dna footprinting dna sequence analysis fish proteins fos genes genetic promoter regions genomics growth hormone humans insulin interleukin-3 introns metallothionein multigene family myc genes nucleic acid databases nucleic acid regulatory sequences nucleic acid sequence homology phylogeny regulator genes transcriptional regulatory elements

SPRINGTool Content

http://algorithm.cs.nthu.edu.tw/tools/SPRING

DNA > Phylogeny Reconstruction
Sequence Comparison > Comparative Genomics

Sorting Permutation by Reversals and Block Interchanges (SPRING) is a tool for the analysis of genome rearrangements. SPRING takes two or more chromosomes as its input and then computes a minimum series of reversals and/or block-interchanges for transforming one chromosome into another. Phylogenetic trees based on the rearrangement analysis are also shown as part of the results.

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tagsalgorithms bacterial chromosomes bacterial genome chromosome inversion chromosome mapping chromosomes dna sequence analysis gammaproteobacteria gene order gene rearrangement genetic models genetic recombination genomics molecular evolution nucleic acid sequence homology phylogeny sequence alignment vibrio

YOGYTool Content

http://www.bahlerlab.info/YOGY/

DNA > Sequence Retrieval and Submission
Model Organisms > Fly
Model Organisms > Microbes
Model Organisms > Mouse and Rat
Model Organisms > Plants
Model Organisms > Yeast
Protein > Sequence Retrieval
Sequence Comparison > Comparative Genomics

Eukaryotic Orthology (YOGY) is a resource for retrieving orthologous proteins from nine eukaryotic organisms. Using a gene or protein identifier as a query, this database provides comprehensive, combined information on orthologs in other species using data from five independent resources: KOGs, Inparanoid, Homologene, OrthoMCL, and a table of curated orthologs between budding yeast and fission yeast. Associated Gene Ontology (GO) terms of orthologs can also be retrieved.

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tagsamino acid sequence homology animals controlled vocabulary genetic databases humans mice proteins rats systems integration

Sequence Comparison > Multiple Sequence Alignments

FISHTool Content

http://max.ucmp.umu.se/sahmm/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.

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tagsamino acid sequence homology markov chains protein databases tertiary protein structure

GenDecoderTool Content

http://darwin.uvigo.es/software/gendecoder.html

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Multiple Sequence Alignments

GenDecoder is a prediction server for animal mitochondrial genetic codes. It provides information about codon-usage, amino acid composition, GC content and a final genetic code prediction for a mitochondrial genome sequence.

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tagsamino acid sequence animals base sequence codon conserved sequence mitochondrial genes molecular evolution protein biosynthesis sequence alignment sequence analysis

HHsenserTool Content

http://toolkit.tuebingen.mpg.de/hhsenser

Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

HHsenser is a tool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, HHSenser is able to build alignments with as many near or remote homologs as possible allowing users to explore protein superfamilies.

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tagsamino acid sequence homology markov chains protein sequence analysis sequence alignment sequence analysis

Kalign, Kalignvu, and MumsaTool Content

http://msa.cgb.ki.se/cgi-bin/msa.cgi

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences. Kalignvu is an xml based alignment viewer that allows users to resize alignments and choose different colour schemes. Mumsa is a tool for automatic assessment of alignment quality.

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tagsalgorithms dna sequence analysis genome genomics nucleic acid databases protein databases protein sequence analysis reproducibility of results roc curve sequence alignment

MAGIIC-PROTool Content

http://biominer.bime.ntu.edu.tw/magiicpro/

Protein > Domains and Motifs
Protein > Sequence Features
Sequence Comparison > Multiple Sequence Alignments

MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented.

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tagsbinding sites ligands molecular models multiprotein complexes protein conformation protein sequence analysis

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

NASTTool Content

http://greengenes.lbl.gov/cgi-bin/nph-NAST_align.cgi

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
RNA > General Resources
Sequence Comparison > Multiple Sequence Alignments

Nearest Alignment Space Termination (NAST) is a multiple sequence alignment server for comparative analysis of 16S rRNA gene sequences from bacteria and archaea.

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tagsalgorithms archaeal genes bacillus anthracis bacterial genes cluster analysis computer-aided design dna probes dna sequence analysis equipment design gene expression profiling nucleic acid sequence homology oligonucleotide array sequence analysis ribosomal rna rrna genes sequence alignment staphylococcus aureus

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

TreeDomViewerTool Content

http://www.bioinformatics.nl/tools/treedom

DNA > Phylogeny Reconstruction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

TreeDomViewer is a tool for the visualization of phylogeny and protein domain structure. TreeDomViewer constructs phylogenetic trees and projects the corresponding protein domain information onto the multiple sequence alignment.

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tagsphylogeny protein sequence analysis proteins sequence alignment software design tertiary protein structure

Sequence Comparison > Other Alignment Tools

ASPicTool Content

http://t.caspur.it/ASPIC/

Expression > Splicing
Expression > cDNA, EST, SAGE
Sequence Comparison > Other Alignment Tools

Alternative Splicing Prediction (ASPic) can predict alternative splicing of user submitted genes based on comparative analysis of available transcript and genome data from a variety of species. Results include graphical and tabular views of the splicing patterns of full-length mRNA isoforms compatible with the detected splice sites of the genes as well as structural and functional annotations.

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tagsalgorithms alternative splicing animals base sequence benchmarking exons gene expression profiling genomics heterogeneous-nuclear ribonucleoproteins humans introns messenger rna molecular computers molecular models protein isoforms rna splice sites sequence alignment software design software validation

HHrepTool Content

http://toolkit.tuebingen.mpg.de/hhrep

Protein > 2-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).

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tagsamino acid repetitive sequences markov chains protein folding protein sequence analysis sequence alignment

PAL2NALTool Content

http://coot.embl.de/pal2nal/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Other Alignment Tools

PAL2NAL converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. Synonymous (Ks) and non-synonymous (Ka) substitution rates can be calculated.

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tagscodon dna sequence analysis exons protein sequence analysis sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Sequence Comparison > Pairwise Sequence Alignments

CrossLinkTool Content

http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.ht...

RNA > Functional RNAs
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

NAR Web Server Issue 2006
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tagsmicrornas rna sequence analysis sequence alignment

FISHTool Content

http://max.ucmp.umu.se/sahmm/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.

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tagsamino acid sequence homology markov chains protein databases tertiary protein structure

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

PlotRepTool Content

http://repeats.abc.hu/cgi-bin/plotrep.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

PlotRep is a tool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphical output.

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tagsgenomics interspersed repetitive sequences

SWAKKTool Content

http://oxytricha.princeton.edu/SWAKK/

DNA > Phylogeny Reconstruction
Protein > 3-D Structural Features
Protein > Phylogeny Reconstruction
Sequence Comparison > Pairwise Sequence Alignments

Sliding Window Analysis of Ka and Ks (SWAKK) is tool for detecting positive selection in proteins using a sliding window substitution rate analysis. The program can display the results on a 3D protein structure.

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tagsamino acid substitution computational biology dna sequence analysis genetic selection protein conformation proteins sequence alignment

Sequence Comparison > Similarity Searching

AlgPredTool Content

http://www.imtech.res.in/raghava/algpred/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.

This content is being maintained by raghavagps.

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tagsalgorithms allergens amino acid motifs amino acids artificial intelligence epitope mapping epitopes immunoglobulin e proteins

BLASTTool Content

http://www.ncbi.nlm.nih.gov/BLAST/

DNA > Gene Prediction
DNA > Sequence Retrieval and Submission
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Similarity Searching

Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

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tagsalgorithms amino acid sequence base sequence factual databases genetic databases genome humans mutation national library of medicine (u.s.) nucleic acid databases nucleic acid sequence homology nucleotides protein databases protein sequence analysis sensitivity and specificity sequence alignment sequence analysis systems integration united states
setsNational Center for Biotechnology Information (NCBI)

Cascade PSI-BlastDatabase Content

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

Protein > Domains and Motifs
Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

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tagsamino acid sequence amino acid sequence homology molecular models molecular sequence data protein conformation protein databases protein folding protein sequence analysis proteins sequence alignment tertiary protein structure

CrossLinkTool Content

http://www-ab.informatik.uni-tuebingen.de/software/crosslink/webstart/welcome.ht...

RNA > Functional RNAs
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Crosslink is a tool for visualizing pairwise sequence similiarity relationships determined using BLAST, Vmatch, and RNAhybrid. The nucleotide sequences and their relationships are displayed as nodes and links of a network, respectively. CrossLink can be useful for investigating potential interactions between microRNAs and their targets.

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tagsmicrornas rna sequence analysis sequence alignment

DOUTfinderDatabase Content

http://mendel.imp.ac.at/dout/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences.

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tagsamino acid sequence homology humans tertiary protein structure

FISHTool Content

http://max.ucmp.umu.se/sahmm/

Protein > 3-D Structure Retrieval/Viewing
Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Family Identification with Structure Anchored HMMs (FISH) is a server for the identification of remote sequence homologues on the basis of protein domains.

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tagsamino acid sequence homology markov chains protein databases tertiary protein structure

FeatureMap3DTool Content

http://www.cbs.dtu.dk/services/FeatureMap3D/

Protein > 3-D Structural Features
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

FeatureMap3D is a tool to map protein features and sequence conservation onto homologous structures in PDB.

NAR Web Server Issue 2006
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tagsamino acid sequence amino acid sequence homology amino acids conserved sequence exons molecular models protein conformation protein databases protein structural homology proteins sequence alignment

FeatureScanTool Content

http://gnaweb.gbf.de/cgi-bin/FeatureScan/FeatureScan.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Similarity Searching

FeatureScan searches for sequence similarity by comparing physico-chemical properties of DNA such as charge, melting enthalpy, conformational parameters, etc.

NAR Web Server Issue 2006
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tagsanimals automated pattern recognition bacterial dna bacterial genes dna dna sequence analysis escherichia coli genetic models genetic promoter regions genomics humans mice nucleic acid sequence homology rats sequence alignment thermodynamics

HHrepTool Content

http://toolkit.tuebingen.mpg.de/hhrep

Protein > 2-D Structure Prediction
Protein > Sequence Features
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

HHrep is a tool for the de novo identification of repeats in protein sequences based on the pairwise comparison of profile hidden Markov models (HMMs).

NAR Web Server Issue 2006
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tagsamino acid repetitive sequences markov chains protein folding protein sequence analysis sequence alignment

HHsenserTool Content

http://toolkit.tuebingen.mpg.de/hhsenser

Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

HHsenser is a tool for sensitive iterative sequence searching based on HMM-HMM comparison. Starting from a single sequence or an alignment, HHSenser is able to build alignments with as many near or remote homologs as possible allowing users to explore protein superfamilies.

NAR Web Server Issue 2006
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tagsamino acid sequence homology markov chains protein sequence analysis sequence alignment sequence analysis

MIGenAS ToolkitTool Content

http://www.migenas.org/

DNA > Phylogeny Reconstruction
DNA > Sequence Retrieval and Submission
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Localization and Targeting
Protein > Phylogeny Reconstruction
Protein > Sequence Retrieval
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Integrated Gene Analysis System (MIGenAS) provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction. Users can also configure \"meta\"-tools as a pipeline of individual tools and intermediate filters.

NAR Web Server Issue 2006
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tagsanimals computational biology genetic databases humans mice sequence alignment sequence analysis systems integration

MPI ToolkitTool Content

http://toolkit.tuebingen.mpg.de

DNA > Phylogeny Reconstruction
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

Max-Planck Institute Bioinformatics Toolkit provides access to many different bioinformatics software tools and databases for sequence similarity searching, multiple sequence alignments, phylogenetic analysis, and protein structure prediction.

This content is being maintained by mremmert.

NAR Web Server Issue 2006
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tagscomputational biology protein conformation protein sequence analysis proteins sequence alignment

Onto-ToolsTool Content

http://vortex.cs.wayne.edu/Projects.html

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Onto-Tools is a suite of tools for data mining based on information from Gene Ontology (GO). Onto-Tools includes an annotation database and the data mining tools: Onto-Express, Onto-Compare, Onto-Design, Onto-Translate, Onto-Miner, Pathway-Express, Promoter-Express, nsSNPCounter, TAQ, and OE2GO; free registration is required.

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tagsanimals bias (epidemiology) binding sites biomedical technology assessment breast neoplasms caenorhabditis elegans computational biology dna sequence analysis drosophila melanogaster equipment failure analysis female gene expression profiling genes genetic databases genetic promoter regions genomics humans mice molecular evolution multigene family neoplasms neoplastic gene expression regulation nucleic acid databases oligonucleotide array sequence analysis programming languages proteins rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism software design statistical data interpretation systems integration transcription factors

PlotRepTool Content

http://repeats.abc.hu/cgi-bin/plotrep.pl

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

PlotRep is a tool for the visual analysis of dispersed genomic repeats. The tool is designed to merge fragments belonging to the same copy of a repeat and allows for the inspection of the results using a dot-plot like graphical output.

NAR Web Server Issue 2006
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tagsgenomics interspersed repetitive sequences

T-COFFEETool Content

http://www.tcoffee.org/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Comparison
Protein > Phylogeny Reconstruction
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Other Alignment Tools
Sequence Comparison > Similarity Searching

The T-COFFEE site includes links to a collection of tools for computing, evaluating, and manipulating multiple alignments of protein sequences and structures. T-COFFEE is a protein multiple sequence alignment tool for sequences with less than 30 percent identity. Expresso (or 3DCoffee) aligns sequences using structural information. M-Coffee is a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Other algorithms provide RNA sequence alignment, and distantly related sequence alignment by homology extension. A consistency based multiple sequence alignment program has been added.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

TACTTool Content

http://jbirc.jbic.or.jp/tact/

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Human Genome > Annotations
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Transcriptome Auto-annotation Conducting Tool (TACT) is an automated tool for conducting functional annotation of transcripts that integrates sequence similarity searches and functional motif predictions. TACT was originally developed as an automatic annotation pipeline for the Human Full-length cDNA Annotation Invitational (H-Inv) project.

NAR Web Server Issue 2006
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tagsalternative splicing amino acid motifs amino acid sequence base sequence complementary dna computational biology dna sequence analysis expressed sequence tags genes genetic databases genetic models genetic polymorphism genetic transcription human genome humans messenger rna microsatellite repeats molecular sequence data nucleic acid databases open reading frames protein databases proteins rna sequence analysis sequence analysis single nucleotide polymorphism systems integration tertiary protein structure

TavernaTool Content

http://taverna.sourceforge.net/

Computer Related > Web Services
DNA > Annotations
DNA > Gene Prediction
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Similarity Searching

Taverna is a tool for creating and running bioinformatics workflows.

NAR Web Server Issue 2006
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tagscomputational biology database management systems genetic databases genomics online systems sequence analysis software design systems integration
setsUniversity of Manchester