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NAR Web Server Issue 2007

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Computer Related

DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

Computer Related > Web Services

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

DNA > Annotations

AsteriasTool Content

http://asterias.bioinfo.cnio.es/

DNA > Annotations
Expression > Transcript Expression Analysis

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.

This content is being maintained by rdiaz02.

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tagsalgorithms animals automated pattern recognition automation cluster analysis computational biology computer simulation database management systems dna sequence analysis gene expression profiling genetic models genomics humans nucleic acid hybridization oligonucleotide array sequence analysis programming languages sequence alignment statistical models

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

FatiGOplusTool Content

http://www.fatigo.org/

DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

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

GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

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tagsanimals computational biology database management systems fungal genes gene expression regulation genetic databases genetic models genome genomics humans programming languages proteomics statistical models

INDELSCANTool Content

http://indelscan.genomics.sinica.edu.tw/IndelScan/

DNA > Annotations
Sequence Comparison > Analysis of Aligned Sequences

INDELSCAN is a tool for genome-wide identification of indels.

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tagsanimals base sequence computational biology genetic polymorphism human genome humans molecular sequence data mutation nucleic acid sequence homology saccharomyces cerevisiae sequence deletion single nucleotide polymorphism species specificity

KAASTool Content

http://www.genome.jp/kegg/kaas/

DNA > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

LTR_FinderTool Content

http://tlife.fudan.edu.cn/ltr_finder/

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Plants

LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.

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tagsalgorithms base sequence computational biology database management systems dna sequence analysis molecular sequence data nucleic acid databases retroelements saccharomyces cerevisiae sequence alignment terminal repeat sequences

MADAPTool Content

http://ccg.vital-it.ch/madap/

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

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tagsalgorithms animals base sequence chromatin immunoprecipitation cluster analysis complementary dna computational biology dna primers eukaryotic cells expressed sequence tags genetic databases genetic promoter regions genome humans nucleic acid databases open reading frames response elements statistical models

NCBI Influenza Virus Sequence Annotation ToolTool Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

DNA > Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.

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tagsalgorithms amino acid sequence dna sequence analysis genotype influenza a virus influenza b virus molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

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

RTAnalyzerTool Content

http://www.riboclub.org/cgi-bin/RTAnalyzer/index.pl?page=rt_find

DNA > Annotations
DNA > Structure and Sequence Feature Detection

RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.

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tagsalgorithms computational biology database management systems dna sequence analysis false positive reactions genetic models long interspersed nucleotide elements nucleic acid databases retroelements sequence alignment terminal repeat sequences

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

DNA > Gene Prediction

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

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tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results rna

DNA > Phylogeny Reconstruction

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

MultiPhylTool Content

http://www.cs.nuim.ie/distributed/multiphyl.php

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.

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tagsalgorithms animals computational biology computer simulation computing methodologies dna sequence analysis genetic databases genetic models genomics humans likelihood functions molecular evolution phylogeny sequence alignment statistical models

PhylemonTool Content

http://phylemon.bioinfo.cipf.es

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an integrated environment to allow for evolutionary analyses, format conversion, file storage and editing capacity, and has saved phylogenetic pipeline function.

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tagsanimals computational biology dna sequence analysis genetic databases genetic techniques humans molecular evolution phylogeny programming languages protein sequence analysis sequence alignment statistical models

SelectonTool Content

http://selecton.tau.ac.il/

DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Selecton is a server for the identification of site-specific positive selection and purifying selection.

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tagsalgorithms amino acid sequence amino acid substitution amino acids animals bayes theorem computational biology computer simulation dna mutational analysis genetic models hiv protease humans molecular evolution molecular models molecular sequence data phylogeny protein sequence analysis proteins site-directed mutagenesis structure-activity relationship

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

DNA > Sequence Polymorphisms

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

QuickSNPTool Content

http://bioinformoodics.jhmi.edu/quickSNP.pl

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.

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tagsalgorithms animals automation chromosome mapping computational biology dna sequence analysis genetic databases genetic models genotype human genome humans linkage disequilibrium single nucleotide polymorphism

StSNPTool Content

http://ilyinlab.org/StSNP/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.

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tagsalgorithms chromosome mapping computational biology database management systems dna sequence analysis genetic databases humans open reading frames protein interaction mapping protein sequence analysis proteins sequence alignment single nucleotide polymorphism

WhETSTool Content

http://www.rothamsted.ac.uk/whets/

DNA > Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching

WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.

This content is being maintained by RowanMitchell.

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tagscomputational biology expressed sequence tags genetic databases genetic models plant chromosomes plant genes plant genome ploidies sequence alignment single nucleotide polymorphism triticum

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

DNA > Sequence Retrieval and Submission

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

NCBI Influenza Virus Sequence Annotation ToolTool Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

DNA > Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.

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tagsalgorithms amino acid sequence dna sequence analysis genotype influenza a virus influenza b virus molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

WhETSTool Content

http://www.rothamsted.ac.uk/whets/

DNA > Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching

WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.

This content is being maintained by RowanMitchell.

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tagscomputational biology expressed sequence tags genetic databases genetic models plant chromosomes plant genes plant genome ploidies sequence alignment single nucleotide polymorphism triticum

DNA > Structure and Sequence Feature Detection

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

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tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

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tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results rna

CRISPRFinderTool Content

http://crispr.u-psud.fr/Server/CRISPRfinder.php

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.

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tagsalgorithms archaeal genome bacterial genome chromosome mapping computational biology database management systems genetic databases intergenic dna nucleic acid repetitive sequences

CodonOTool Content

http://digbio.missouri.edu/software/index.html

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

CodonO is a method for measuring synonymous codon usage bias within and across genomes.

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tagsarchaeal dna archaeal genome bacterial dna bacterial genome base composition codon computational biology computer simulation gc rich sequence genetic code genetic models genome species specificity

DSHIFTTool Content

http://www.chem.cuhk.edu.hk/DSHIFT/

DNA > Structure and Sequence Feature Detection

DSHIFT is a web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.

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tagsalgorithms base sequence biomolecular nuclear magnetic resonance carbon computational biology computer simulation dna magnetic resonance spectroscopy molecular models molecular sequence data molecular structure nucleic acid conformation oligonucleotides phosphorus programming languages protons reproducibility of results sensitivity and specificity stochastic processes temperature

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

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

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

LTR_FinderTool Content

http://tlife.fudan.edu.cn/ltr_finder/

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Plants

LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.

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tagsalgorithms base sequence computational biology database management systems dna sequence analysis molecular sequence data nucleic acid databases retroelements saccharomyces cerevisiae sequence alignment terminal repeat sequences

MYBSTool Content

http://cg1.iis.sinica.edu.tw/~mybs/index.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Yeast

MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.

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tagsalgorithms base sequence binding sites computational biology dna sequence analysis gene targeting molecular sequence data oligonucleotide array sequence analysis protein binding saccharomyces cerevisiae saccharomyces cerevisiae proteins sequence alignment transcription factors

MelinaIITool Content

http://melina2.hgc.jp/public/index.html

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

MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.

This content is being maintained by Kenta Nakai.

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tagsalgorithms amino acid motifs animals computational biology database management systems dna sequence analysis genetic promoter regions humans proteins sequence alignment

OPTIMIZERTool Content

http://genomes.urv.es/OPTIMIZER/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression

OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.

This content is being maintained by ppuigbo.

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tagsalgorithms animals base sequence codon computational biology dna dna sequence analysis gene expression gene expression regulation molecular sequence data protein biosynthesis ribosomes

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

PAPTool Content

http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do

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

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

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RF_DYMHCTool Content

http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htm

DNA > Structure and Sequence Feature Detection
Model Organisms > Yeast

RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.

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RTAnalyzerTool Content

http://www.riboclub.org/cgi-bin/RTAnalyzer/index.pl?page=rt_find

DNA > Annotations
DNA > Structure and Sequence Feature Detection

RTAnalyzer is an application to find new retroposons and detect L1 retroposition signatures.

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SCOPETool Content

http://genie.dartmouth.edu/scope/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE does not have any nuisance parameters so does not require the user to guess what the results might be. SCOPE is also very robust to noisy data and is still 50% as accurate even in the presence of 4-fold noise. SCOPE can also identify other genes in the genome that might be coregulated with the original gene set.

This content is being maintained by bobgross.

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STAMPTool Content

http://www.benoslab.pitt.edu/stamp/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.

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tagsamino acid motifs animals base sequence binding sites cluster analysis computational biology dna dna sequence analysis humans molecular sequence data multigene family protein binding saccharomyces cerevisiae sequence alignment transcription factors

VISTATool Content

http://genome.lbl.gov/vista/index.shtml

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

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tagsalgorithms animals base sequence binding sites cats cattle chickens chromosome mapping computational biology dna dna sequence analysis dogs exons gene expression profiling genome genomics human chromosomes human genome humans kinesin leukemia mice molecular evolution molecular sequence data nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology pan troglodytes papio phylogeny rabbits rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism swine takifugu time factors transcription factors untranslated regions zebrafish

WebMOTIFSTool Content

http://fraenkel.mit.edu/webmotifs/

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

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

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ZiFiTTool Content

http://bindr.gdcb.iastate.edu/ZiFiT/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

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oPOSSUMTool Content

http://www.cisreg.ca/oPOSSUM_new/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.

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DNA > Tools For the Bench

NTMGTool Content

http://oblab.cs.nchu.edu.tw:8080/WebSDL/

DNA > Tools For the Bench

NTMG (N-Terminal Truncated Mutants Generator) is a tool for generating multiplex PCR primers for designing N-terminal truncated mutants.

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OligoCalcTool Content

http://www.basic.northwestern.edu/biotools/OligoCalc.html

DNA > Tools For the Bench

OligoCalc calculates the physical properties of single- and double-stranded DNA and RNA molecules including melting temperature (multiple methods), concentration, molecular weight, and absorbance at 260 nanometers. OligoCalc can also account for 5’ and 3’ chemical modifications and predict potential hairpin loop formation.

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Primer ZTool Content

http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.

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Primer3PlusTool Content

http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi

DNA > Tools For the Bench

Primer3Plus is an enhanced web interface to the popular Primer3 PCR primer design program.

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REPKTool Content

http://rocaplab.ocean.washington.edu/tools/repk

DNA > Tools For the Bench
Model Organisms > Microbes

REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.

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WebTraceMinerTool Content

http://www.conifergdb.org/software/wtm1.2/

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE

WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3\' and 5\' termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.

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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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tagscomputational biology directories as topic factual databases genetic databases genetics humans molecular biology
setsOntario Institute for Cancer Research (OICR)

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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Expression > Gene Regulation

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

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tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Protein > Interactions, Pathways, Enzymes

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

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FatiGOplusTool Content

http://www.fatigo.org/

DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

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Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

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

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

MADAPTool Content

http://ccg.vital-it.ch/madap/

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

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MYBSTool Content

http://cg1.iis.sinica.edu.tw/~mybs/index.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Yeast

MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.

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MelinaIITool Content

http://melina2.hgc.jp/public/index.html

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

MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.

This content is being maintained by Kenta Nakai.

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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

PAPTool Content

http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do

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

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

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SCOPETool Content

http://genie.dartmouth.edu/scope/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SCOPE (Suite for Computational identification Of Promoter Elements) is a set of programs aimed at identifying novel cis-regulatory elements from groups of upstream sequences. SCOPE does not have any nuisance parameters so does not require the user to guess what the results might be. SCOPE is also very robust to noisy data and is still 50% as accurate even in the presence of 4-fold noise. SCOPE can also identify other genes in the genome that might be coregulated with the original gene set.

This content is being maintained by bobgross.

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tagsalgorithms amino acid motifs amino acid sequence homology artificial intelligence automated pattern recognition base sequence binding sites cluster analysis computational biology computer simulation consensus sequence conserved sequence dna dna sequence analysis gene expression profiling gene expression regulation genetic models genetic promoter regions molecular sequence data oligonucleotide array sequence analysis predictive value of tests protein binding proteins response elements saccharomyces cerevisiae sequence alignment statistical models transcription factors transcriptional regulatory elements

STAMPTool Content

http://www.benoslab.pitt.edu/stamp/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.

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tagsamino acid motifs animals base sequence binding sites cluster analysis computational biology dna dna sequence analysis humans molecular sequence data multigene family protein binding saccharomyces cerevisiae sequence alignment transcription factors

WebMOTIFSTool Content

http://fraenkel.mit.edu/webmotifs/

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

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

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tagsalgorithms amino acid motifs animals automated pattern recognition automation base sequence bayes theorem binding sites chromatin immunoprecipitation cluster analysis computational biology conserved sequence dna dna sequence analysis gene expression profiling humans mice molecular sequence data protein binding saccharomyces cerevisiae sequence alignment transcription factors

ZiFiTTool Content

http://bindr.gdcb.iastate.edu/ZiFiT/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ZiFiT (Zinc Finger Targeter) assists in the design of zinc finger proteins that can bind to specific DNA sequences. ZiFiT has been updated to integrate additional tools and resources including scoring schemes for modular assembly, an interface with the Zinc Finger Database of engineered ZFPs, and direct query of NCBI BLAST servers for identification of potential off-target sites within a host genome.

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tagsbinding sites computational biology deoxyribonucleases dna sequence analysis dna-binding proteins humans protein conformation protein engineering secondary protein structure tertiary protein structure transcription factors zinc fingers

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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oPOSSUMTool Content

http://www.cisreg.ca/oPOSSUM_new/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.

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Expression > Gene Set Analysis

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

Expression > Networks

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

Expression > Protein Expression

OPTIMIZERTool Content

http://genomes.urv.es/OPTIMIZER/

DNA > Structure and Sequence Feature Detection
Expression > Protein Expression

OPTIMIZER is an application that optimizes the codon usage of a DNA sequence. This server can be used to predict and optimize the level expression of a gene in heterologous gene expression systems.

This content is being maintained by ppuigbo.

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VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

Expression > Splicing

AStalavistaTool Content

http://genome.imim.es/astalavista/

Expression > Splicing

AStalavista (alternative splicing transcriptional landscape visualization tool) dynamically identifies, extracts, and displays alternative splicing events from whole genome annotations and user provided gene sets.

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tagsalternative splicing chromosome mapping computational biology dna probes dna sequence analysis genetic databases genome humans messenger rna oligonucleotide array sequence analysis rna splice sites

SplicePortTool Content

http://spliceport.cs.umd.edu/

Expression > Splicing

SplicePort makes splice-site predictions for submitted sequences, and allows browsing of the motifs used in the prediction. Feature selection is optimized for human splice sites.

This content is being maintained by rnainfo.

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tagsautomated pattern recognition base sequence chromosome mapping computational biology computer simulation dna dna sequence analysis genetic models genome humans molecular sequence data rna splice sites sequence alignment

Expression > Transcript Expression Analysis

AsteriasTool Content

http://asterias.bioinfo.cnio.es/

DNA > Annotations
Expression > Transcript Expression Analysis

Asterias is a set of tools for the analyses of high throughput genomic data that includes applications for microarray data normalization, filtering, detection of differential gene expression, class and survival prediction model building, and analysis of array CGH data. Most applications use parallel computing resulting in significant increases in speed.

This content is being maintained by rdiaz02.

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tagsalgorithms animals automated pattern recognition automation cluster analysis computational biology computer simulation database management systems dna sequence analysis gene expression profiling genetic models genomics humans nucleic acid hybridization oligonucleotide array sequence analysis programming languages sequence alignment statistical models

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Protein > Interactions, Pathways, Enzymes

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

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FatiGOplusTool Content

http://www.fatigo.org/

DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

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

GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

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tagsanimals computational biology database management systems fungal genes gene expression regulation genetic databases genetic models genome genomics humans programming languages proteomics statistical models

MAGMATool Content

http://www.magma-fgcz.unizh.ch/pages/loginuser.jsf

Expression > Transcript Expression Analysis

MAGMA can be used for the analyses of two-channel microarray experiments and computes genes with significant differential expression using R and Bioconductor. Automatically generated R-scripts are available for download.

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tagsalgorithms computational biology database management systems gene expression profiling oligonucleotide array sequence analysis programming languages software design statistical models

OSCARTool Content

http://biocomp.bioen.uiuc.edu/oscar/

Expression > Transcript Expression Analysis

OSCAR (Open System for Clustering Analysis) is a platform for cluster analysis of microarray data.

NAR Web Server Issue 2007
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tagsaging algorithms alzheimer disease animals biological models computational biology eye proteins genetic models homeodomain proteins humans insulin receptor nad(p)h dehydrogenase (quinone) neurons oligonucleotide array sequence analysis paired box transcription factors repressor proteins species specificity

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

PAPTool Content

http://bioinformatics.wustl.edu/webTools/portalModule/PromoterSearch.do

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

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.

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tagsalgorithms animals cell proliferation cholesterol chromatin immunoprecipitation computational biology conserved sequence gene expression profiling gene expression regulation genetic databases genetic models genetic promoter regions genetic transcription humans mice protein binding transcription factors

PathExpressTool Content

http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/

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

PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.

This content is being maintained by ngoffard.

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tagsalgorithms animals biological models computational biology database management systems enzymes gene expression profiling humans medicago truncatula metabolic networks and pathways metabolism oligonucleotide array sequence analysis protein interaction mapping

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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tagsalgorithms animals computational biology dna gene expression profiling genomics humans messenger rna oligonucleotide array sequence analysis statistical data interpretation

Expression > cDNA, EST, SAGE

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Protein > Interactions, Pathways, Enzymes

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

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tagsalgorithms animals biological models computational biology computer simulation gene expression profiling genetic models humans phenotype protein interaction mapping signal transduction statistical data interpretation

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

GeneHub-GEPISTool Content

http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat

GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.

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tagsalgorithms biological tumor markers chromosome mapping dna sequence analysis expressed sequence tags gene expression profiling genetic testing humans neoplasms online systems sequence alignment

WebTraceMinerTool Content

http://www.conifergdb.org/software/wtm1.2/

DNA > Tools For the Bench
Expression > cDNA, EST, SAGE

WebTraceMiner is a tool for processing and mining Expressed Sequence Tag (EST) trace files. It can help characterize 3\' and 5\' termini of cDNA inserts by detecting sequence features such as vector fragments, adapter/linker sequences, insert-flanking restriction endonuclease recognition sites, and polyA or polyT tails.

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tagsalgorithms animals base sequence complementary dna computational biology dna sequence analysis expressed sequence tags gene expression profiling genetic databases molecular sequence data sequence alignment

Human Genome > Annotations

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

NAR Web Server Issue 2007
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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

MADAPTool Content

http://ccg.vital-it.ch/madap/

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations

MADAP is a clustering tool for the interpretation annotation data mapped onto complete or partial genome sequences. Initially developed for determining transcription start sites (TSS) by defining 5\' and 3\'ends of mRNA, MADAP also has utility in clustering other annotation data types (ChIP-chip data, for example).

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tagsalgorithms animals base sequence chromatin immunoprecipitation cluster analysis complementary dna computational biology dna primers eukaryotic cells expressed sequence tags genetic databases genetic promoter regions genome humans nucleic acid databases open reading frames response elements statistical models

Human Genome > Health and Disease

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

FluGenomeTool Content

http://www.flugenome.org/

Human Genome > Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching

FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

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tagscomputational biology genetic databases genetic polymorphism genomics genotype influenza a virus orthomyxoviridae phylogeny viral genes viral genome viral proteins

G2DTool Content

http://www.ogic.ca/projects/g2d_2/

Human Genome > Health and Disease

G2D (Candidate Genes to Inherited Diseases) scans a human genomic region for genes related to an inherited disease. The G2D server also presents precomputed candidate genes for more than 600 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene.

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tagsalgorithms alzheimer disease asthma chromosome mapping computational biology genes genetic databases genetic linkage genetic markers genetic predisposition to disease human genome humans inborn genetic diseases mathematics medline obesity phenotype type 2 diabetes mellitus

Human Genome > Other Resources

GeneHub-GEPISTool Content

http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat

GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.

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tagsalgorithms biological tumor markers chromosome mapping dna sequence analysis expressed sequence tags gene expression profiling genetic testing humans neoplasms online systems sequence alignment

LIPID MAPSTool Content

http://www.lipidmaps.org/tools/index.html

Human Genome > Other Resources
Other Molecules > Metabolites

LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.

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tagsanimals chemical models computational biology database management systems factual databases glycosphingolipids humans isomerism lipid metabolism lipids mice molecular conformation molecular structure polysaccharides protein databases proteome proteomics terminology as topic

Human Genome > Sequence Polymorphisms

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

Primer ZTool Content

http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.

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tagsalgorithms automation computational biology dna primers exons genetic databases genetic promoter regions genetic techniques humans messenger rna polymerase chain reaction single nucleotide polymorphism

QuickSNPTool Content

http://bioinformoodics.jhmi.edu/quickSNP.pl

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

QuickSNP is a resource for the selection of tagSNPs in the human genome that includes a gene-centric selection module.

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tagsalgorithms animals automation chromosome mapping computational biology dna sequence analysis genetic databases genetic models genotype human genome humans linkage disequilibrium single nucleotide polymorphism

StSNPTool Content

http://ilyinlab.org/StSNP/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.

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tagsalgorithms chromosome mapping computational biology database management systems dna sequence analysis genetic databases humans open reading frames protein interaction mapping protein sequence analysis proteins sequence alignment single nucleotide polymorphism

Literature > Search Tools

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

eTBLASTDatabase Content

http://etest.vbi.vt.edu/etblast3/

Literature > Search Tools

eTBLAST is a textual similarity search engine. This server can parse and summarize the results of an abstract similarity search to find appropriate journals for publication, authors with expertise in a given field, and documents similar to a submitted query.

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tagsalgorithms artificial intelligence authorship automated pattern recognition bibliographic databases controlled vocabulary database management systems humans informatics medline natural language processing peer review periodicals as topic publications publishing pubmed software design

Literature > Text Mining and Semantics

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

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tagsanimals biology computational biology database management systems factual databases genetic databases humans programming languages systems integration

iHOPTool Content

http://www.ihop-net.org/UniPub/iHOP/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.

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tagsanimals arabidopsis biology biomedical engineering caenorhabditis elegans computational biology database management systems drosophila melanogaster escherichia coli genes humans mice natural language processing periodicals as topic publications pubmed signal transduction software design zebrafish

Model Organisms > General Resources

CodonOTool Content

http://digbio.missouri.edu/software/index.html

DNA > Structure and Sequence Feature Detection
Model Organisms > General Resources

CodonO is a method for measuring synonymous codon usage bias within and across genomes.

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tagsarchaeal dna archaeal genome bacterial dna bacterial genome base composition codon computational biology computer simulation gc rich sequence genetic code genetic models genome species specificity

Model Organisms > Microbes

CRISPRFinderTool Content

http://crispr.u-psud.fr/Server/CRISPRfinder.php

DNA > Structure and Sequence Feature Detection
Model Organisms > Microbes

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Finder detects this family of direct repeats found in the DNA of many bacteria and archaea.

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tagsalgorithms archaeal genome bacterial genome chromosome mapping computational biology database management systems genetic databases intergenic dna nucleic acid repetitive sequences

MobilomeFINDERTool Content

http://mml.sjtu.edu.cn/MobilomeFINDER/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.

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tagsalgorithms bacterial genes bacterial genome bacterial rna computational biology enterobacteriaceae escherichia coli escherichia coli k12 fungal gene expression regulation genomic islands genomics oligonucleotide array sequence analysis polymerase chain reaction pseudomonas aeruginosa shigella shigella flexneri streptococcus suis theoretical models transfer rna

REPKTool Content

http://rocaplab.ocean.washington.edu/tools/repk

DNA > Tools For the Bench
Model Organisms > Microbes

REPK (Restriction Endonuclease Picker) assists in the choice of restriction endonucleases for terminal restriction fragment length polymorphism (T-RFLP) by finding sets of four restriction endonucleases which together uniquely differentiate user-designated sequence groups.

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tagsalgorithms bacteria bacterial dna computational biology ecosystem enzymes factual databases microbiology phylogeny restriction fragment length polymorphism ribosomal dna ribosomal rna

Model Organisms > Mouse and Rat

GeneHub-GEPISTool Content

http://www.cgl.ucsf.edu/Research/genentech/genehub-gepis/

Expression > cDNA, EST, SAGE
Human Genome > Other Resources
Model Organisms > Mouse and Rat

GeneHub-GEPIS is a tool for inferring human and mouse gene expression patterns based on normalized EST abundance in various normal and cancerous tissues.

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tagsalgorithms biological tumor markers chromosome mapping dna sequence analysis expressed sequence tags gene expression profiling genetic testing humans neoplasms online systems sequence alignment

Primer ZTool Content

http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do

DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Model Organisms > Mouse and Rat

Primer Z is an interface for PCR primer design for human, mouse, or rat genes and human SNPs; uses Primer3 primer design program.

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tagsalgorithms automation computational biology dna primers exons genetic databases genetic promoter regions genetic techniques humans messenger rna polymerase chain reaction single nucleotide polymorphism

Model Organisms > Other Organisms

FluGenomeTool Content

http://www.flugenome.org/

Human Genome > Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching

FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

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tagscomputational biology genetic databases genetic polymorphism genomics genotype influenza a virus orthomyxoviridae phylogeny viral genes viral genome viral proteins

NCBI Influenza Virus Sequence Annotation ToolTool Content

http://www.ncbi.nlm.nih.gov/genomes/FLU/Database/annotation.cgi

DNA > Annotations
DNA > Sequence Retrieval and Submission
Model Organisms > Other Organisms

The NCBI Influenza Virus Sequence Annotation Tool is a web application for user-provided sequences. It can predict protein sequences encoded by an input flu sequence and produce a feature table that can be used for sequence submission to GenBank.

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tagsalgorithms amino acid sequence dna sequence analysis genotype influenza a virus influenza b virus molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

Model Organisms > Plants

LTR_FinderTool Content

http://tlife.fudan.edu.cn/ltr_finder/

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Model Organisms > Plants

LTR_Finder (Long Terminal Repeat Finder) is an efficient program for finding full-length LTR retrotransposons in genome sequences.

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tagsalgorithms base sequence computational biology database management systems dna sequence analysis molecular sequence data nucleic acid databases retroelements saccharomyces cerevisiae sequence alignment terminal repeat sequences

WhETSTool Content

http://www.rothamsted.ac.uk/whets/

DNA > Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching

WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.

This content is being maintained by RowanMitchell.

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tagscomputational biology expressed sequence tags genetic databases genetic models plant chromosomes plant genes plant genome ploidies sequence alignment single nucleotide polymorphism triticum

Model Organisms > Yeast

MYBSTool Content

http://cg1.iis.sinica.edu.tw/~mybs/index.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Model Organisms > Yeast

MYBS (Mining Yeast Binding Sites) is a tool for mapping Transcription factors (TFs) and their binding sites (TFBSs) that integrates both experimentally verified (ChIP-chip data) and predicted position weight matrixes (PWMs) from several databases.

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tagsalgorithms base sequence binding sites computational biology dna sequence analysis gene targeting molecular sequence data oligonucleotide array sequence analysis protein binding saccharomyces cerevisiae saccharomyces cerevisiae proteins sequence alignment transcription factors

RF_DYMHCTool Content

http://www.bioinf.seu.edu.cn/Recombination/rf_dymhc.htm

DNA > Structure and Sequence Feature Detection
Model Organisms > Yeast

RF_DYMHC (Random Forest-Based System for Detecting Yeast Meiotic Recombination Hotspots and Coldspots) predicts recombination hot/cold spots in the yeast genome.

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tagsalgorithms artificial intelligence automated pattern recognition chromosome mapping codon computational biology dna sequence analysis fungal genome genetic recombination meiosis nucleotides saccharomyces cerevisiae

Other Molecules > Metabolites

LIPID MAPSTool Content

http://www.lipidmaps.org/tools/index.html

Human Genome > Other Resources
Other Molecules > Metabolites

LIPID Metabolites And Pathways Strategy (LIPID MAPS) is a consortium that presents a collection of tools for performing tasks such as drawing lipid structures and predicting possible structures from mass spectrometry data.

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tagsanimals chemical models computational biology database management systems factual databases glycosphingolipids humans isomerism lipid metabolism lipids mice molecular conformation molecular structure polysaccharides protein databases proteome proteomics terminology as topic

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

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tagsadenosine triphosphate algorithms animals archaea bacteria biological evolution biological models cell physiological phenomena chemical models coenzymes computational biology computer simulation energy metabolism eukaryotic cells factual databases gene expression profiling genetic models genetic variation glucose glycolysis humans inorganic chemicals kinetics metabolism molecular evolution nerve net organic chemicals phosphates phylogeny physiological adaptation protein biosynthesis proteins signal transduction species specificity substrate specificity

Other Molecules > Small Molecules

FrogTool Content

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

Other Molecules > Small Molecules

Frog (Free Online Drug Conformation) is a service aimed at generating 3D conformations for drug-like compounds starting from their 1D or 2D descriptions (smiles or sdf).

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tagsalgorithms chemical models chemistry computational biology computer simulation ligands molecular conformation molecular structure pharmaceutical chemistry pliability protein databases proteins quantitative structure-activity relationship x-ray crystallography

Protein > 2-D Structure Prediction

OpenHUSARTool Content

http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.start...

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching

Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).

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tagsalgorithms computational biology protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

Pcons.netTool Content

http://pcons.net/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.

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tagsalgorithms amino acid sequence animals automatic data processing automation computational biology computer simulation consensus sequence humans molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins roc curve secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

PhobiusTool Content

http://phobius.sbc.su.se/

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

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.

This content is being maintained by lukall.

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tagsalgorithms artificial intelligence computational biology computer simulation cytoplasm markov chains membrane proteins molecular models probability programming languages protein conformation protein databases protein sorting signals proteomics secondary protein structure statistical models theoretical models

PrDOSTool Content

http://prdos.hgc.jp/cgi-bin/top.cgi

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

PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence artificial intelligence automated pattern recognition computational biology computing methodologies human immunodeficiency virus nef gene products molecular sequence data nef gene products protein conformation protein databases protein sequence analysis proteins sequence alignment statistical models

iPDATool Content

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

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

iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology cluster analysis computational biology computer simulation escherichia coli humans molecular models molecular sequence data protein databases protein sequence analysis proteins secondary protein structure sequence alignment

Protein > 3-D Structural Features

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

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tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins tertiary protein structure

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

KNOTSTool Content

http://knots.mit.edu/

Protein > 3-D Structural Features

KNOTS is a web server that detects knots in protein structures.

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tagsalgorithms bacterial proteins computational biology computer simulation cysteine endopeptidases genetic databases haemophilus influenzae humans molecular evolution molecular models protein binding protein conformation protein databases protein folding proteins statistical models tertiary protein structure

PDB2PQR ServerTool Content

http://pdb2pqr.sourceforge.net/

Protein > 3-D Structural Features
Protein > Biochemical Features

Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.

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tagscomputational biology computer simulation hydrogen hydrogen bonding ligands mathematical computing molecular conformation molecular structure programming languages protein databases proteins solvents static electricity

PFPTool Content

http://pfp.technion.ac.il/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

This content is being maintained by shulash3.

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tagsalgorithms amino acid motifs amino acid sequence binding sites computational biology dna-binding proteins hydrogen bonding hydrogen-ion concentration molecular conformation molecular models molecular sequence data neural networks (computer) plant proteins programming languages protein binding protein conformation protein databases proteins static electricity surface properties viral proteins

PI2PETool Content

http://pipe.scs.fsu.edu/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

PICTool Content

http://crick.mbu.iisc.ernet.in/~PIC/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.

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tagsamino acids animals computational biology humans hydrogen bonding molecular conformation molecular models molecular structure plant proteins protein databases proteins

ProMateusTool Content

http://bioportal.weizmann.ac.il/promate/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.

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tagsalgorithms binding sites computational biology dna factual databases molecular models protein binding protein conformation proteins secondary protein structure surface properties

Protein Dipole ServerTool Content

http://bioportal.weizmann.ac.il/dipol/

Protein > 3-D Structural Features
Protein > Biochemical Features

The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.

This content is being maintained by Clifford Felder.

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tagsbibliographic databases biophysics computational biology computer simulation enzymes fungal proteins mathematics molecular models protein conformation protein databases proteins secondary protein structure statistical models

RCITool Content

http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.py

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

RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.

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tagsalgorithms animals biomolecular nuclear magnetic resonance carbon isotopes computational biology computer simulation humans hydrogen magnetic resonance spectroscopy molecular conformation nitrogen isotopes pliability protein conformation proteins reproducibility of results statistical models

StSNPTool Content

http://ilyinlab.org/StSNP/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.

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tagsalgorithms chromosome mapping computational biology database management systems dna sequence analysis genetic databases humans open reading frames protein interaction mapping protein sequence analysis proteins sequence alignment single nucleotide polymorphism

eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp

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

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

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tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

pKNOTTool Content

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

Protein > 3-D Structural Features

pKNOT (Protein Knot) is a tool that can detect knots in proteins as well as providing information on knotted proteins in PDB.

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tagsalgorithms computational biology computer simulation molecular models phytochrome protein conformation protein databases protein folding proteins statistical models

Protein > 3-D Structure Comparison

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

DBAliDatabase Content

http://salilab.org/DBAli/

Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Domains and Motifs

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.

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tagsalgorithms amino acid sequence amino acid sequence homology computational biology molecular sequence data protein conformation protein databases protein sequence analysis proteins pseudomonas aeruginosa sequence alignment software design statistical data interpretation structure-activity relationship

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

QSCOP - BLASTTool Content

http://qscop-blast.services.came.sbg.ac.at/

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

QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).

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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

eF-seekTool Content

http://ef-site.hgc.jp/eF-seek/index.jsp

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

eF-seek predicts protein functional sites by searching for similar electrostatic potential and molecular surface shapes against eF-site, a database of electrostatic surfaces for representative ligand binding sites.

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tagsalgorithms antibodies binding sites biological models computational biology computer simulation database management systems ligands molecular models protein conformation protein databases protein folding proteins proteomics s-adenosylhomocysteine static electricity structure-activity relationship three-dimensional imaging trypsin

fastSCOPTool Content

http://gemdock.life.nctu.edu.tw/fastSCOP/

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.

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tagsamino acid sequence amino acid sequence homology computational biology molecular evolution molecular models molecular sequence data protein conformation protein databases protein sequence analysis protein structural homology proteins statistical data interpretation tertiary protein structure

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

Protein > 3-D Structure Prediction

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

M4TTool Content

http://manaslu.aecom.yu.edu/M4T/

Protein > 3-D Structure Prediction

M4T (Multiple Mapping Method with Multiple Templates) is a comparative protein structure modeling server that uses a combination of multiple templates and iterative optimization of alternative alignments.

NAR Web Server Issue 2007
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tagsalgorithms amino acid sequence biological models computational biology computer simulation molecular models molecular sequence data protein sequence analysis proteins secondary protein structure sequence alignment theoretical models

MODPROPEPTool Content

http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.html

Protein > 3-D Structure Prediction
Protein > Domains and Motifs

MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.

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tagsalgorithms animals computational biology computer simulation humans major histocompatibility complex peptides protein conformation protein databases proteins x-ray crystallography

NQ-FlipperTool Content

https://flipper.services.came.sbg.ac.at/cgi-bin/flipper.php

Protein > 3-D Structure Prediction

NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures.

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tagsamides asparagine computational biology crystallography escherichia coli glutamine molecular conformation molecular models protein conformation protein databases protein folding proteins reproducibility of results statistical data interpretation stereoisomerism structural models thermodynamics

Pcons.netTool Content

http://pcons.net/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.

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tagsalgorithms amino acid sequence animals automatic data processing automation computational biology computer simulation consensus sequence humans molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins roc curve secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

PrDOSTool Content

http://prdos.hgc.jp/cgi-bin/top.cgi

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

PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.

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tagsalgorithms amino acid sequence artificial intelligence automated pattern recognition computational biology computing methodologies human immunodeficiency virus nef gene products molecular sequence data nef gene products protein conformation protein databases protein sequence analysis proteins sequence alignment statistical models

ProSA-webTool Content

https://prosa.services.came.sbg.ac.at/prosa.php

Protein > 3-D Structure Prediction

ProSA-web (Protein Structure Analysis) is an extension of the classic ProSA program used for the refinement and validation of experimental protein structures and in structure prediction and modeling.

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tagscomputational biology escherichia coli molecular conformation molecular models protein conformation protein databases protein denaturation protein folding proteins sequence analysis

RCITool Content

http://wishart.biology.ualberta.ca/rci/cgi-bin/rci_cgi_1_d.py

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

RCI (Random Coil Index) is a method for predicting protein flexibility using secondary chemical shifts.

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tagsalgorithms animals biomolecular nuclear magnetic resonance carbon isotopes computational biology computer simulation humans hydrogen magnetic resonance spectroscopy molecular conformation nitrogen isotopes pliability protein conformation proteins reproducibility of results statistical models

iPDATool Content

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

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

iPDA (Integrated Protein Disorder Analyzer) predicts disordered regions of a query protein sequence.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology cluster analysis computational biology computer simulation escherichia coli humans molecular models molecular sequence data protein databases protein sequence analysis proteins secondary protein structure sequence alignment

Protein > 3-D Structure Retrieval/Viewing

MinActionPathTool Content

http://lorentz.immstr.pasteur.fr/joel/index.php

Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

MinActionPath calculates the most-probable trajectory between two known structural states of a protein.

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tagsalgorithms amino acid sequence biological models chemical models computational biology computer simulation energy transfer molecular models molecular sequence data protein conformation proteins tertiary protein structure theoretical models thermodynamics

MolProbityTool Content

http://molprobity.biochem.duke.edu/

Protein > 3-D Structure Retrieval/Viewing
RNA > Structure Prediction, Visualization, and Design

MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.

This content is being maintained by dcrjsr.

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tagscomputational biology hydrogen bonding hydrogens molecular graphics molecular models molecular structure nucleic acid conformation protein protein conformation reproducibility of results rna structure validation three-dimensional imaging

PMGTool Content

http://bioserv.rpbs.jussieu.fr/~autin/cgi-bin/PMG

Protein > 3-D Structure Retrieval/Viewing

The Protein Movie Generator (PMG) is a tool to generate protein pictures, animations, and movies.

This content is being maintained by ludovicautin.

NAR Web Server Issue 2007
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tagscomputational biology computer simulation ligands motion motion pictures as topic programming languages protein folding proteins rotation time factors vibration

QSCOP - BLASTTool Content

http://qscop-blast.services.came.sbg.ac.at/

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

QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).

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tagsalgorithms amino acid sequence chemical models computational biology computer simulation molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins pyrococcus furiosus sequence alignment structure-activity relationship thermotoga maritima

Protein > Annotation and Function

DBAliDatabase Content

http://salilab.org/DBAli/

Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Domains and Motifs

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.

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tagsalgorithms amino acid sequence amino acid sequence homology computational biology molecular sequence data protein conformation protein databases protein sequence analysis proteins pseudomonas aeruginosa sequence alignment software design statistical data interpretation structure-activity relationship

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

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tagsanimals computational biology database management systems fungal genes gene expression regulation genetic databases genetic models genome genomics humans programming languages proteomics statistical models

SEPACSTool Content

http://fred.bioinf.uni-sb.de/sepacs.html

Protein > Annotation and Function

SEPACS (Seroreactivity Pattern Classification System) is a a web-based application for classification of seroreactivity profiles.

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tagsalgorithms bayes theorem blood proteins brain neoplasms computational biology dna genetic markers glioma humans meningioma mutation neoplastic gene expression regulation oligonucleotide array sequence analysis sensitivity and specificity

Sequence HarmonyTool Content

http://www.ibi.vu.nl/programs/seqharmwww/

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

Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites computational biology conserved sequence entropy membrane transport proteins molecular models molecular sequence data protein sequence analysis proteins ras proteins secondary protein structure sequence alignment smad proteins

Protein > Biochemical Features

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

PDB2PQR ServerTool Content

http://pdb2pqr.sourceforge.net/

Protein > 3-D Structural Features
Protein > Biochemical Features

Server that allows users to convert PDB files into PQR files by adding missing atoms, optimizing hydrogen bonding and assigning atomic charge and radius parameters. The resulting PQR file can be used for electrostatic calculations which can give insight into the influence of electrostatics on biomolecular structures.

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tagscomputational biology computer simulation hydrogen hydrogen bonding ligands mathematical computing molecular conformation molecular structure programming languages protein databases proteins solvents static electricity

PI2PETool Content

http://pipe.scs.fsu.edu/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

ProSight PTMTool Content

http://prosightptm2.scs.uiuc.edu/

Protein > Biochemical Features
Protein > Proteomics

ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the \'Top-Down\' tandem mass spectrometry (MS/MS) approach.

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tagsalternative splicing amino acid sequence animals automatic data processing computational biology genetic polymorphism humans mass spectrometry molecular sequence data post-translational protein processing programming languages protein databases protein sequence analysis proteins ribosomal proteins saccharomyces cerevisiae proteins sequence tagged sites

Protein Dipole ServerTool Content

http://bioportal.weizmann.ac.il/dipol/

Protein > 3-D Structural Features
Protein > Biochemical Features

The Protein Dipole server calculates and displays the net charge, dipole moment and mean radius of any 3-dimensional protein structure.

This content is being maintained by Clifford Felder.

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tagsbibliographic databases biophysics computational biology computer simulation enzymes fungal proteins mathematics molecular models protein conformation protein databases proteins secondary protein structure statistical models

Protein > Domains and Motifs

3dLOGOTool Content

http://3dlogo.uniroma2.it/3dLOGO/home.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs

3dLOGO is a server for the identification and analysis of conserved protein three-dimensional (3D) substructures.

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tagsalgorithms amino acid motifs amino acid sequence animals automation binding sites computational biology computer simulation conserved sequence factual databases false negative reactions humans molecular models molecular structure programming languages protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins sensitivity and specificity sequence alignment src homology domains statistical models surface properties

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

DBAliDatabase Content

http://salilab.org/DBAli/

Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Domains and Motifs

DBAli is a database that includes a comprehensive all-against-all comparison of protein structures in the PDB database. Tools associated with the database allow users to mine this protein structure space by establishing relationships between protein structures and their functions.

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tagsalgorithms amino acid sequence amino acid sequence homology computational biology molecular sequence data protein conformation protein databases protein sequence analysis proteins pseudomonas aeruginosa sequence alignment software design statistical data interpretation structure-activity relationship

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

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tagsanimals computational biology database management systems fungal genes gene expression regulation genetic databases genetic models genome genomics humans programming languages proteomics statistical models

Gibbs Motif SamplerTool Content

http://ccmbweb.ccv.brown.edu/gibbs/gibbs.html

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

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).

This content is being maintained by bbth.

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tagsalgorithms amino acid sequence animals bacterial dna bacterial genes bacterial genome bacterial outer membrane proteins base sequence binding sites biological evolution carrier proteins chemical models computational biology consensus sequence dna sequence analysis escherichia coli factual databases gammaproteobacteria gene expression regulation genetic models genetic transcription genetic variation helix-loop-helix motifs homology human genome humans markov chains mice molecular sequence data monte carlo method nonparametric statistics nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology phylogeny protein binding protein prenylation secondary protein structure sequence alignment skeletal muscle statistical models transcription factors transcription initiation site transferases

KinasePhos 2.0Tool Content

http://kinasephos2.mbc.nctu.edu.tw/

Protein > Domains and Motifs

KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.

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tagscatalytic domain computational biology computer simulation markov chains neural networks (computer) phosphoproteins phosphorylation probability protein kinases protein sequence analysis sensitivity and specificity

MODPROPEPTool Content

http://www.nii.res.in/~narendra/PROT_PEP_INTERACTION/index.html

Protein > 3-D Structure Prediction
Protein > Domains and Motifs

MODPROPEP is a server for structural modeling of protein kinases and MHC proteins in complex with their substrate peptides.

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MelinaIITool Content

http://melina2.hgc.jp/public/index.html

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

MelinaII (Motif Elucidator in Nucleotide Sequence Assembly) can run multiple motif prediction tools (Consensus, MEME, Gibbs Sampler, MDScan, Weeder) simultaneously. Graphical results can be used to compare predictions of potential DNA motifs (such as transcription factor binding sites, TFBS) in promoter regions.

This content is being maintained by Kenta Nakai.

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tagsalgorithms amino acid motifs animals computational biology database management systems dna sequence analysis genetic promoter regions humans proteins sequence alignment

MyHitsTool Content

http://myhits.isb-sib.ch

Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments

The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.

This content is being maintained by myhits.

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tagscomputational biology programming languages protein databases protein sequence analysis sequence alignment systems integration tertiary protein structure

OpenHUSARTool Content

http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.start...

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching

Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).

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Pcons.netTool Content

http://pcons.net/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.

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tagsalgorithms amino acid sequence animals automatic data processing automation computational biology computer simulation consensus sequence humans molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins roc curve secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

QSCOP - BLASTTool Content

http://qscop-blast.services.came.sbg.ac.at/

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

QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).

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RNABindRTool Content

http://bindr.gdcb.iastate.edu/RNABindR/

Protein > Domains and Motifs

RNABindR is a server for analyzing and predicting RNA binding sites in proteins.

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tagsamino acid motifs amino acid sequence amino acids animals artificial intelligence bayes theorem binding sites computational biology humans molecular models molecular sequence data predictive value of tests protein conformation protein databases protein sequence analysis proteins reproducibility of results rna sensitivity and specificity

SH3-HunterTool Content

http://cbm.bio.uniroma2.it/SH3-Hunter/

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

SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.

This content is being maintained by enricoferraro.

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tagsalgorithms amino acid motifs amino acid sequence animals artificial intelligence automated pattern recognition binding sites chemical models computational biology computer simulation factual databases humans ligands molecular models molecular sequence data multigene family neural networks (computer) peptide fragments peptide library peptides probability protein binding protein interaction mapping protein sequence analysis proteins proteome sensitivity and specificity sequence alignment src homology domains structure-activity relationship substrate specificity tertiary protein structure

SLiMDiscTool Content

http://bioware.ucd.ie/~slimdisc/

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

SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.

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tagsamino acid motifs amino acid sequence amino acid sequence homology animals biological models computational biology computer simulation humans molecular evolution molecular sequence data protein sequence analysis proteins rats

WebMOTIFSTool Content

http://fraenkel.mit.edu/webmotifs/

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

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

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tagsalgorithms amino acid motifs animals automated pattern recognition automation base sequence bayes theorem binding sites chromatin immunoprecipitation cluster analysis computational biology conserved sequence dna dna sequence analysis gene expression profiling humans mice molecular sequence data protein binding saccharomyces cerevisiae sequence alignment transcription factors

fastSCOPTool Content

http://gemdock.life.nctu.edu.tw/fastSCOP/

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.

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tagsamino acid sequence amino acid sequence homology computational biology molecular evolution molecular models molecular sequence data protein conformation protein databases protein sequence analysis protein structural homology proteins statistical data interpretation tertiary protein structure

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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Protein > Interactions, Pathways, Enzymes

3D-partnerTool Content

http://3d-partner.life.nctu.edu.tw/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

3D-partner is a tool to predict interacting partners and binding models of a query protein sequence through the analysis of structural complexes.

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tagsamino acid sequence amino acid sequence homology binding sites gene expression profiling molecular sequence data protein binding protein databases protein interaction mapping protein sequence analysis proteins saccharomyces cerevisiae saccharomyces cerevisiae proteins tertiary protein structure

CARGOTool Content

http://cargo2.bioinfo.cnio.es/docs/aboutCargo.html

DNA > Annotations
DNA > Sequence Polymorphisms
Human Genome > Annotations
Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

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DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

DEEPTool Content

http://www.bioinf.med.uni-goettingen.de/services/deep/

Expression > Gene Regulation
Expression > Transcript Expression Analysis
Expression > cDNA, EST, SAGE
Protein > Interactions, Pathways, Enzymes

DEEP (Differential Expression Effector Prediction) is a tool that can identify effectors of specific expression profiles by combining gene expression data with biological expert knowledge about biomolecular interaction networks (provided by resources like TRANSPATH, for example).

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ESTExplorerTool Content

http://estexplorer.biolinfo.org

DNA > Annotations
DNA > Structure and Sequence Feature Detection
Expression > cDNA, EST, SAGE
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

ESTExplorer is an automated suite of programs to pre-process, assemble and functionally annotate ESTs at both DNA and protein level.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis expressed sequence tags female genetic databases genomics haemonchus humans male nucleic acid databases oligonucleotide array sequence analysis programming languages untranslated regions

FatiGOplusTool Content

http://www.fatigo.org/

DNA > Annotations
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

FatiGOplus is a tool for the functional profiling of genome-scale experiments oriented to the interpretation of microarray experiments. As part of the Babelomics suite, FatiGOplus finds differential distributions of biological terms (GO, KEGG pathways, Interpro motifs, Transfac motifs, CisRed motifs, etc.) between two groups of genes.

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GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

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KAASTool Content

http://www.genome.jp/kegg/kaas/

DNA > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

MetaPath OnlineTool Content

http://scopes.biologie.hu-berlin.de/

Other Molecules > Metabolites
Protein > Interactions, Pathways, Enzymes

MetaPath Online gives users access to an algorithm for network expansion. Starting with given metabolites, called seed compounds, the algorithm uses known information about metabolic reactions and pathways to expand the network and define scope. This systematic investigation of structure-function relationships of metabolic networks can offer evolutionary insights.

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tagsadenosine triphosphate algorithms animals archaea bacteria biological evolution biological models cell physiological phenomena chemical models coenzymes computational biology computer simulation energy metabolism eukaryotic cells factual databases gene expression profiling genetic models genetic variation glucose glycolysis humans inorganic chemicals kinetics metabolism molecular evolution nerve net organic chemicals phosphates phylogeny physiological adaptation protein biosynthesis proteins signal transduction species specificity substrate specificity

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

PFPTool Content

http://pfp.technion.ac.il/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

PFP (Patch Finder Plus) is a tool for extracting and displaying positive electrostatic patches on protein surfaces which can be indicative of nucleic acid binding interfaces.

This content is being maintained by shulash3.

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tagsalgorithms amino acid motifs amino acid sequence binding sites computational biology dna-binding proteins hydrogen bonding hydrogen-ion concentration molecular conformation molecular models molecular sequence data neural networks (computer) plant proteins programming languages protein binding protein conformation protein databases proteins static electricity surface properties viral proteins

PI2PETool Content

http://pipe.scs.fsu.edu/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Interactions, Pathways, Enzymes

PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids animals artificial intelligence binding sites biomolecular nuclear magnetic resonance computational biology computer simulation dna dna-binding proteins factual databases genomic library hydrophobic and hydrophilic interactions membrane proteins molecular conformation molecular models molecular sequence data mutation mycoplasma neural networks (computer) open reading frames prions protein binding protein conformation protein sequence analysis proteins quaternary protein structure reproducibility of results rna-binding proteins saccharomyces cerevisiae secondary protein structure sequence alignment solvents

PICTool Content

http://crick.mbu.iisc.ernet.in/~PIC/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

Protein Interactions Calculator (PIC) is a server which recognizes various kinds of interactions; such as disulphide bonds, hydrophobic interactions, hydrogen bonds, aromatic interactions, and ionic interactions within a protein or between proteins in a complex.

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tagsamino acids animals computational biology humans hydrogen bonding molecular conformation molecular models molecular structure plant proteins protein databases proteins

PathExpressTool Content

http://bioinfoserver.rsbs.anu.edu.au/utils/PathExpress/

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

PathExpress is a tool developed to interpret gene expression data obtained from microarray experiments by identifying and visualizing the most relevant metabolic pathways associated with a subset of genes (e.g. differentially expressed genes). Enzyme Neighborhood (a sub-network of linked enzymes with a limited path length) allows identification of the most relevant sub-network affected in a gene expression experiment.

This content is being maintained by ngoffard.

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tagsalgorithms animals biological models computational biology database management systems enzymes gene expression profiling humans medicago truncatula metabolic networks and pathways metabolism oligonucleotide array sequence analysis protein interaction mapping

ProMateusTool Content

http://bioportal.weizmann.ac.il/promate/

Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

ProMateus extends ProMate, a protein binding site predictor, and allows the user to suggest new features that might improve the prediction of the binding site locations.

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SH3-HunterTool Content

http://cbm.bio.uniroma2.it/SH3-Hunter/

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

SH3-Hunter identifies putative SH3 domain interaction sites on protein sequences.

This content is being maintained by enricoferraro.

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tagsalgorithms amino acid motifs amino acid sequence animals artificial intelligence automated pattern recognition binding sites chemical models computational biology computer simulation factual databases humans ligands molecular models molecular sequence data multigene family neural networks (computer) peptide fragments peptide library peptides probability protein binding protein interaction mapping protein sequence analysis proteins proteome sensitivity and specificity sequence alignment src homology domains structure-activity relationship substrate specificity tertiary protein structure

SLiMDiscTool Content

http://bioware.ucd.ie/~slimdisc/

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

SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.

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tagsamino acid motifs amino acid sequence amino acid sequence homology animals biological models computational biology computer simulation humans molecular evolution molecular sequence data protein sequence analysis proteins rats

StSNPTool Content

http://ilyinlab.org/StSNP/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > 3-D Structural Features
Protein > Interactions, Pathways, Enzymes

StSNP (Structure SNP) is a server which provides the ability to analyze and compare human nonsynonymous SNPs (nsSNP) in protein structures, protein complexes, protein-protein interfaces and metabolic networks.

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tagsalgorithms chromosome mapping computational biology database management systems dna sequence analysis genetic databases humans open reading frames protein interaction mapping protein sequence analysis proteins sequence alignment single nucleotide polymorphism

VisANTTool Content

http://visant.bu.edu/

Expression > Gene Set Analysis
Expression > Networks
Expression > Protein Expression
Expression > Transcript Expression Analysis
Protein > Interactions, Pathways, Enzymes

VisANT is an integrative visual analysis tool for biological networks and pathways that contains modules for querying and integrating KEGG pathways with expression data. VisANT is java-based, and can be run as a java applet, as a java web application, or downloaded and run locally. New functions in VisANT 3.5 allow determination of over-representation and expression enrichment.

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tagsalgorithms animals biological models caenorhabditis elegans cell cycle computational biology computer simulation database management systems drosophila fungal genes gene expression profiling gene expression regulation gene regulatory networks genetic databases genetic models genetic transcription genome helminth genes helminth proteins humans macromolecular substances metabolism mice protein databases protein interaction mapping proteome saccharomyces cerevisiae saccharomyces cerevisiae proteins signal transduction software design systems integration three-dimensional imaging transcription factors two-hybrid system techniques

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

g:ProfilerTool Content

http://biit.cs.ut.ee/gprofiler/

DNA > Annotations
DNA > Sequence Polymorphisms
Expression > Gene Regulation
Expression > Transcript Expression Analysis
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

g:Profiler is a set of tools for functional annotation of gene lists that includes: g:GOSt, which retrieves the most significant Gene Ontology (GO) terms, KEGG and REACTOME pathways, and TRANSFAC motifs; g:Convert, for conversion between gene or protein names/IDs; g:Orth, for retrieving orthologs; and, g:Sorter, which searches for similar expression profiles. Functional analysis of SNPs and other DNA polymorphisms is also supported, as is enrichment analysis.

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iHOPTool Content

http://www.ihop-net.org/UniPub/iHOP/

Literature > Text Mining and Semantics
Protein > Interactions, Pathways, Enzymes

iHOP (Information Hyperlinked over Proteins) allows researchers to explore a network of gene and protein interactions based on published scientific literature. For each gene search, iHOP reports sentences from abstracts associating it with other genes, links out to full abstracts, and reports experimental evidence for the interactions, if available. You can also select sentences to create and visualize your own gene model.

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tagsanimals arabidopsis biology biomedical engineering caenorhabditis elegans computational biology database management systems drosophila melanogaster escherichia coli genes humans mice natural language processing periodicals as topic publications pubmed signal transduction software design zebrafish

Protein > Localization and Targeting

GeneTrailTool Content

http://genetrail.bioinf.uni-sb.de/index.php

DNA > Annotations
Expression > Transcript Expression Analysis
Protein > Annotation and Function
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Protein > Localization and Targeting

GeneTrail analyzes gene sets for statistically significant accumulations of genes belonging to functional categories. Two common statistical approaches are implemented including: Over-Representation Analysis (ORA) for comparing a reference set of genes to a test set; and, Gene Set Enrichment Analysis (GSEA) for scoring sorted lists of genes.

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tagsanimals computational biology database management systems fungal genes gene expression regulation genetic databases genetic models genome genomics humans programming languages proteomics statistical models

OpenHUSARTool Content

http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.start...

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching

Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).

NAR Web Server Issue 2007
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tagsalgorithms computational biology protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

PhobiusTool Content

http://phobius.sbc.su.se/

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

Phobius is a combined transmembrane topology and signal peptide predictor. The server also allows for constrained and homology-enriched predictions.

This content is being maintained by lukall.

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tagsalgorithms artificial intelligence computational biology computer simulation cytoplasm markov chains membrane proteins molecular models probability programming languages protein conformation protein databases protein sorting signals proteomics secondary protein structure statistical models theoretical models

SLiMDiscTool Content

http://bioware.ucd.ie/~slimdisc/

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

SLiMDisc (Short Linear Motif Discovery) is a tool for finding shared motifs in proteins with a common attribute such as sub-cellular location or a common interaction partner.

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tagsamino acid motifs amino acid sequence amino acid sequence homology animals biological models computational biology computer simulation humans molecular evolution molecular sequence data protein sequence analysis proteins rats

WoLF PSORTTool Content

http://wolfpsort.org/

Protein > Localization and Targeting

WoLF PSORT is an extension of the PSORT II program for protein subcellular location prediction.

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tagsarabidopsis computational biology humans membrane proteins programming languages protein databases protein sequence analysis protein sorting signals proteins reproducibility of results secondary protein structure statistical models

Protein > Molecular Dynamics and Docking

FastContactTool Content

http://structure.pitt.edu/servers/fastcontact/

Protein > Molecular Dynamics and Docking

FastContact is a free energy scoring tool for protein-protein complex structures.

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tagsalgorithms amino acids binding sites biological models chemical models computational biology computer simulation hydrogen bonding molecular models protein binding protein conformation protein interaction mapping protein sequence analysis proteins solvents static electricity thermodynamics

MinActionPathTool Content

http://lorentz.immstr.pasteur.fr/joel/index.php

Protein > 3-D Structure Retrieval/Viewing
Protein > Molecular Dynamics and Docking

MinActionPath calculates the most-probable trajectory between two known structural states of a protein.

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tagsalgorithms amino acid sequence biological models chemical models computational biology computer simulation energy transfer molecular models molecular sequence data protein conformation proteins tertiary protein structure theoretical models thermodynamics

Protein > Phylogeny Reconstruction

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp

Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

MultiPhylTool Content

http://www.cs.nuim.ie/distributed/multiphyl.php

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.

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tagsalgorithms animals computational biology computer simulation computing methodologies dna sequence analysis genetic databases genetic models genomics humans likelihood functions molecular evolution phylogeny sequence alignment statistical models

PhylemonTool Content

http://phylemon.bioinfo.cipf.es

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an integrated environment to allow for evolutionary analyses, format conversion, file storage and editing capacity, and has saved phylogenetic pipeline function.

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tagsanimals computational biology dna sequence analysis genetic databases genetic techniques humans molecular evolution phylogeny programming languages protein sequence analysis sequence alignment statistical models

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 > 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

Multi-QTool Content

http://ms.iis.sinica.edu.tw/Multi-Q-Web/

Protein > Proteomics

Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.

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tagsautomatic data processing computational biology humans ions jurkat cells liquid chromatography mass spectrometry multiprotein complexes peptides protein folding proteins proteomics

ProSight PTMTool Content

http://prosightptm2.scs.uiuc.edu/

Protein > Biochemical Features
Protein > Proteomics

ProSight PTM allows identification and characterization of intact proteins and their post- translational modifications (PTMs) using data from the \'Top-Down\' tandem mass spectrometry (MS/MS) approach.

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tagsalternative splicing amino acid sequence animals automatic data processing computational biology genetic polymorphism humans mass spectrometry molecular sequence data post-translational protein processing programming languages protein databases protein sequence analysis proteins ribosomal proteins saccharomyces cerevisiae proteins sequence tagged sites

Protein > Sequence Features

BioBayesNetTool Content

http://biwww3.informatik.uni-freiburg.de:8080/BioBayesNet/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Protein > Sequence Features

BioBayesNet is a server for feature extraction and Bayesian network modeling of biological sequence data.

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tagsalgorithms amino acid sequence automated pattern recognition bayes theorem binding sites chemical models computational biology computer simulation dna sequence analysis genetic models molecular models molecular sequence data protein binding protein conformation protein folding protein sequence analysis proteins sequence alignment statistical models structure-activity relationship transcription factors

CanPredictTool Content

http://www.cgl.ucsf.edu/Research/genentech/canpredict/

Human Genome > Health and Disease
Human Genome > Sequence Polymorphisms
Protein > Sequence Features

CanPredict uses a combination of computational methods to predict whether specific sequence changes in a protein are likely to be cancer-associated mutations.

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tagsalgorithms alleles amino acids computational biology expressed sequence tags genetic predisposition to disease humans missense mutation neoplasm dna neoplasms single nucleotide polymorphism tumor cell line

WebMOTIFSTool Content

http://fraenkel.mit.edu/webmotifs/

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

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.

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tagsalgorithms amino acid motifs animals automated pattern recognition automation base sequence bayes theorem binding sites chromatin immunoprecipitation cluster analysis computational biology conserved sequence dna dna sequence analysis gene expression profiling humans mice molecular sequence data protein binding saccharomyces cerevisiae sequence alignment transcription factors

Protein > Sequence Retrieval

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

RNA > Functional RNAs

CPCTool Content

http://cpc.cbi.pku.edu.cn/programs/run_cpc.jsp

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
RNA > Functional RNAs

CPC (Coding Potential Calculator) distinguishes protein-coding from non-coding RNAs based on the sequence features of the input transcripts.

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tagsanimals computational biology expressed sequence tags genetic code genetic transcription genetic variation genetic vectors messenger rna mice molecular sequence data nucleic acid databases protein biosynthesis proteins reproducibility of results rna

TFAMTool Content

http://tfam.lcb.uu.se/

RNA > Functional RNAs

TFAM is a system to classify the function of tRNAs that is based on tRNA structural alignments.

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tagsalphaproteobacteria animals bacterial dna bacterial genome computational biology drosophila melanogaster genetic variation genomics histidine-trna ligase horizontal gene transfer molecular evolution nucleic acid databases phylogeny statistical models transfer rna

miPredTool Content

http://www.bioinf.seu.edu.cn/miRNA/

RNA > Functional RNAs

miPred (microRNA Predictor) can distinguish between real and pseudo microRNA precursors.

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tagsanimals base sequence computational biology computer simulation false positive reactions genome genomics humans messenger rna micrornas molecular sequence data nucleic acid conformation species specificity

taveRNATool Content

http://compbio.cs.sfu.ca/taverna/

RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.

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tagsadenosine triphosphatases algorithms antisense rna bacterial genome bacterial rna base sequence binding sites cation transport proteins chemical models computational biology computer simulation escherichia coli escherichia coli proteins humans molecular sequence data nucleic acid conformation plasmids programming languages rna rna sequence analysis rna stability sequence alignment statistical models trans-activators

RNA > Motifs

DIALTool Content

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

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.

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tagsalgorithms base pairing computational biology nucleic acid conformation programming languages protein databases rna rna sequence analysis sequence alignment statistical models

RADARTool Content

http://datalab.njit.edu/biodata/rna/RSmatch/server.htm

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.

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tagsalgorithms base sequence computational biology computer simulation conserved sequence genetic databases humans molecular sequence data nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment untranslated rna

RNA > Sequence Retrieval

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

RNA > Structure Prediction, Visualization, and Design

DIALTool Content

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

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

DIAL (dihedral alignment) is a server that provides access to a dynamic programming algorithm for structural alignment of RNA.

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tagsalgorithms base pairing computational biology nucleic acid conformation programming languages protein databases rna rna sequence analysis sequence alignment statistical models

INFO-RNATool Content

http://www.bioinf.uni-freiburg.de/Software/INFO-RNA/start.html

RNA > Structure Prediction, Visualization, and Design

INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.

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tagsalgorithms base sequence chemical models computational biology computer simulation molecular models molecular sequence data nucleic acid conformation rna rna sequence analysis sequence alignment

MolProbityTool Content

http://molprobity.biochem.duke.edu/

Protein > 3-D Structure Retrieval/Viewing
RNA > Structure Prediction, Visualization, and Design

MolProbity is a structure validation web service for diagnosing problems in 3D models of proteins, nucleic acids or complexes. It adds and optimizes H atoms (correcting 180° flipped Asn/Gln/His sidechains), and then calculates global and local validation for all-atom contacts (steric clashes, H-bonds & vdW), covalent geometry, and conformation (Ramachandran & rotamers for protein, ribose puckers & suite conformers for RNA). Results are displayed online as 3D graphics and sortable charts.

This content is being maintained by dcrjsr.

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tagscomputational biology hydrogen bonding hydrogens molecular graphics molecular models molecular structure nucleic acid conformation protein protein conformation reproducibility of results rna structure validation three-dimensional imaging

RADARTool Content

http://datalab.njit.edu/biodata/rna/RSmatch/server.htm

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

RADAR (RNA Data Analysis and Research) provides multiple tools for RNA structure analysis including: pairwise structure alignment, multiple structure alignment, constrained structure alignment, database searching, and prediction of the consensus structure for a set of RNA sequences.

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tagsalgorithms base sequence computational biology computer simulation conserved sequence genetic databases humans molecular sequence data nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment untranslated rna

RNA MoviesTool Content

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

RNA > Structure Prediction, Visualization, and Design

RNA Movies is a tool for the visualization of RNA secondary structure spaces. The program creates an interpolated animation of user provided sets of secondary structure data.

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tagsalgorithms bacterial rna computational biology computer simulation data display multimedia natronobacterium nucleic acid conformation programming languages rna

RNAborTool Content

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

RNA > Structure Prediction, Visualization, and Design

RNAbor is a server for computing structural neighbors of a RNA secondary structure.

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tagscluster analysis computational biology computer simulation conserved sequence genetic databases molecular sequence data nucleic acid conformation nucleic acid sequence homology ribonucleic acid regulatory sequences rna rna sequence analysis sequence alignment untranslated rna

RNAzTool Content

http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.

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tagsalgorithms archaea base sequence computational biology consensus sequence conserved sequence escherichia coli genome molecular evolution molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny prokaryotic cells ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis rna stability sequence alignment thermodynamics untranslated rna

pknotsRGTool Content

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

RNA > Structure Prediction, Visualization, and Design

pknotsRG is a server for single sequence RNA secondary structure prediction including pseudoknots; source code, binary executable, and web service available.

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tagsalgorithms computational biology computer simulation genetic models hepatitis delta virus nucleic acid conformation predictive value of tests programming languages rna statistical models thermodynamics viral rna

taveRNATool Content

http://compbio.cs.sfu.ca/taverna/

RNA > Functional RNAs
RNA > Structure Prediction, Visualization, and Design

taveRNA hosts three RNA web services: alteRNA, inteRNA and pRuNA. alteRNA is an alternative to many RNA folding methods. inteRNA predicts the joint secondary structure of two RNA sequences. pRuNA is an database pruning method which given a query RNA returns only a few ncRNAs as potential regulators.

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tagsadenosine triphosphatases algorithms antisense rna bacterial genome bacterial rna base sequence binding sites cation transport proteins chemical models computational biology computer simulation escherichia coli escherichia coli proteins humans molecular sequence data nucleic acid conformation plasmids programming languages rna rna sequence analysis rna stability sequence alignment statistical models trans-activators

Sequence Comparison > Alignment Editing and Visualization

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

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp

Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

INDELSCANTool Content

http://indelscan.genomics.sinica.edu.tw/IndelScan/

DNA > Annotations
Sequence Comparison > Analysis of Aligned Sequences

INDELSCAN is a tool for genome-wide identification of indels.

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tagsanimals base sequence computational biology genetic polymorphism human genome humans molecular sequence data mutation nucleic acid sequence homology saccharomyces cerevisiae sequence deletion single nucleotide polymorphism species specificity

MultiPhylTool Content

http://www.cs.nuim.ie/distributed/multiphyl.php

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

MultiPhyl is a high-throughput Maximum Likelihood based phylogeny analysis program that allows researchers to create a virtual phylogenetic supercomputer from a group semi-idle desktop machines.

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tagsalgorithms animals computational biology computer simulation computing methodologies dna sequence analysis genetic databases genetic models genomics humans likelihood functions molecular evolution phylogeny sequence alignment statistical models

RNAzTool Content

http://rna.tbi.univie.ac.at/cgi-bin/RNAz.cgi

RNA > Structure Prediction, Visualization, and Design
Sequence Comparison > Analysis of Aligned Sequences

RNAz detects functional RNA secondary structures in multiple sequence alignments based on thermodynamic stability and structural conservation.

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tagsalgorithms archaea base sequence computational biology consensus sequence conserved sequence escherichia coli genome molecular evolution molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology phylogeny prokaryotic cells ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis rna stability sequence alignment thermodynamics untranslated rna

SelectonTool Content

http://selecton.tau.ac.il/

DNA > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences

Selecton is a server for the identification of site-specific positive selection and purifying selection.

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tagsalgorithms amino acid sequence amino acid substitution amino acids animals bayes theorem computational biology computer simulation dna mutational analysis genetic models hiv protease humans molecular evolution molecular models molecular sequence data phylogeny protein sequence analysis proteins site-directed mutagenesis structure-activity relationship

Sequence HarmonyTool Content

http://www.ibi.vu.nl/programs/seqharmwww/

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

Sequence Harmony detects subfamily specific functional sites from a multiple sequence alignment by scoring compositional differences between given subfamily groupings.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites computational biology conserved sequence entropy membrane transport proteins molecular models molecular sequence data protein sequence analysis proteins ras proteins secondary protein structure sequence alignment smad proteins

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

VISTATool Content

http://genome.lbl.gov/vista/index.shtml

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

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tagsalgorithms animals base sequence binding sites cats cattle chickens chromosome mapping computational biology dna dna sequence analysis dogs exons gene expression profiling genome genomics human chromosomes human genome humans kinesin leukemia mice molecular evolution molecular sequence data nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology pan troglodytes papio phylogeny rabbits rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism swine takifugu time factors transcription factors untranslated regions zebrafish

eProbalignTool Content

http://probalign.njit.edu/probalign/login

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.

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tagsalgorithms amino acid sequence amino acid sequence homology animals computational biology computer simulation dna genetic databases humans molecular sequence data probability protein sequence analysis sequence alignment software design statistical models temperature thermodynamics

Sequence Comparison > Comparative Genomics

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

DAVID Bioinformatics ResourcesTool Content

http://david.abcc.ncifcrf.gov/home.jsp

DNA > Annotations
Expression > Gene Regulation
Human Genome > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

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tagsalgorithms automated pattern recognition computational biology gene expression profiling genetic databases genomics hiv-1 humans macrophages mononuclear leukocytes nucleic acid databases oligonucleotide array sequence analysis statistical data interpretation

KAASTool Content

http://www.genome.jp/kegg/kaas/

DNA > Annotations
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Comparative Genomics

KAAS (KEGG Automatic Annotation Server) is a tool for ortholog assignment and pathway mapping. KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

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tagsanimals artificial intelligence automation chromosome mapping computational biology controlled vocabulary database management systems documentation genome humans proteome sequence analysis signal transduction

MobilomeFINDERTool Content

http://mml.sjtu.edu.cn/MobilomeFINDER/

Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MobilomeFINDER (Mobile Genome FINDER) is a tool for high-throughput genomic island discovery.

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tagsalgorithms bacterial genes bacterial genome bacterial rna computational biology enterobacteriaceae escherichia coli escherichia coli k12 fungal gene expression regulation genomic islands genomics oligonucleotide array sequence analysis polymerase chain reaction pseudomonas aeruginosa shigella shigella flexneri streptococcus suis theoretical models transfer rna

VISTATool Content

http://genome.lbl.gov/vista/index.shtml

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

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tagsalgorithms animals base sequence binding sites cats cattle chickens chromosome mapping computational biology dna dna sequence analysis dogs exons gene expression profiling genome genomics human chromosomes human genome humans kinesin leukemia mice molecular evolution molecular sequence data nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology pan troglodytes papio phylogeny rabbits rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism swine takifugu time factors transcription factors untranslated regions zebrafish

Sequence Comparison > Multiple Sequence Alignments

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

Berkeley Phylogenomics GroupTool Content

http://phylogenomics.berkeley.edu/

DNA > Phylogeny Reconstruction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

The Berkeley Phylogenomics Group provides a series of web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals artificial intelligence bayes theorem binding sites computational biology gene expression profiling genetic databases genetic models humans likelihood functions markov chains molecular evolution molecular sequence data phylogeny protein conformation protein databases protein sequence analysis proteins reproducibility of results sensitivity and specificity sequence alignment src homology domains statistical models tertiary protein structure time factors

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp

Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

MyHitsTool Content

http://myhits.isb-sib.ch

Protein > Domains and Motifs
Sequence Comparison > Multiple Sequence Alignments

The MyHits server integrates several tools with a focus on protein annotation and the analysis of protein domains. Guest users have access to tools such as ClustalW and T-Coffee and databases like Swiss-Prot, Prosite and Interpro. Registration allows users to store their results in private databases, and is free for academic users.

This content is being maintained by myhits.

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tagscomputational biology programming languages protein databases protein sequence analysis sequence alignment systems integration tertiary protein structure

PROMALS and PROMALS3DTool Content

http://prodata.swmed.edu/promals3d

Sequence Comparison > Multiple Sequence Alignments

PROMALS (Profile Multiple Alignment with Local Structure) is a progressive mutliple sequence alignment method that improves alignment quality by using additional homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.

This content is being maintained by jiminpei.

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tagsalgorithms amino acid sequence amino acid sequence homology computational biology conserved sequence molecular sequence data protein sequence analysis protein structural homology proteins reproducibility of results sensitivity and specificity sequence alignment

PhylemonTool Content

http://phylemon.bioinfo.cipf.es

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments

Phylemon is a server that integrates a suite of tools for multiple sequence alignment, phylogeny, and evolutionary tests from the most popular stand-alone phylogenetic and evolutionary analysis programs. Phylemon 2.0 has an integrated environment to allow for evolutionary analyses, format conversion, file storage and editing capacity, and has saved phylogenetic pipeline function.

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tagsanimals computational biology dna sequence analysis genetic databases genetic techniques humans molecular evolution phylogeny programming languages protein sequence analysis sequence alignment statistical models

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

VISTATool Content

http://genome.lbl.gov/vista/index.shtml

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments

VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.

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tagsalgorithms animals base sequence binding sites cats cattle chickens chromosome mapping computational biology dna dna sequence analysis dogs exons gene expression profiling genome genomics human chromosomes human genome humans kinesin leukemia mice molecular evolution molecular sequence data nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology pan troglodytes papio phylogeny rabbits rats reproducibility of results sensitivity and specificity sequence alignment single nucleotide polymorphism swine takifugu time factors transcription factors untranslated regions zebrafish

eProbalignTool Content

http://probalign.njit.edu/probalign/login

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

eProbalign computes maximal expected accuracy multiple sequence alignments from partition function posterior probabilities. eProbalign also provides a platform to visualize the alignment, generate images, and manipulate the output.

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tagsalgorithms amino acid sequence amino acid sequence homology animals computational biology computer simulation dna genetic databases humans molecular sequence data probability protein sequence analysis sequence alignment software design statistical models temperature thermodynamics

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

Sequence Comparison > Other Alignment Tools

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 > Similarity Searching

BLASTOTool Content

http://oxytricha.princeton.edu/BlastO/index.html

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

BLASTO (BLAST on Orthologous groups) is a modified BLAST tool for searching orthologous group data. It treats each orthologous group as a unit and outputs a ranked list of orthologous groups instead of single sequences.

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tagsalgorithms animals automated pattern recognition computational biology genetic databases genome genomics humans nucleic acid sequence homology phylogeny species specificity

COMPASSTool Content

http://prodata.swmed.edu/compass/compass.php

Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Similarity Searching

COMPASS (Comparison of Multiple Protein Alignments with Assessment of Statistical Significance) is a tool for detecting remote levels of sequence similarity using profile-based comparison of multiple sequence alignments. Statistics and speed have been improved, and visualization tools introduced.

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tagsamino acid motifs amino acid sequence amino acid sequence homology capsid proteins clathrin computational biology mamastrovirus molecular evolution molecular models molecular sequence data protein conformation protein databases protein structural homology proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment statistical data interpretation statistics as topic tertiary protein structure trna methyltransferases

EBI ToolsTool Content

http://www.ebi.ac.uk/Tools/webservices/

Computer Related > Web Services
DNA > Sequence Retrieval and Submission
Education > Directories and Portals
Literature > Search Tools
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Sequence Retrieval
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

EBI Tools is a project that aims to provide programmatic access to the various databases and retrieval and analysis services that the European Bioinformatics Institute (EBI) provides through Simple Object Access Protocol (SOAP) and other related web service technologies.

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tagsbibliographic databases biotechnology computational biology europe genetic databases nucleic acids protein sequence analysis proteins sequence alignment sequence analysis sequence homology systems integration

FGFTool Content

http://fgf.genomics.org.cn/service/index.jsp

Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

FGF (Fishing Gene Family) is a resource for finding gene families given a set of protein sequences by investigating phylogenetic trees, duplication fate, and selective pressure (ka/ks calculations).

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tagsalgorithms animals chromosome mapping chromosomes computational biology gene duplication genetic models genome humans molecular evolution phylogeny

FluGenomeTool Content

http://www.flugenome.org/

Human Genome > Health and Disease
Model Organisms > Other Organisms
Sequence Comparison > Similarity Searching

FluGenome is a tool for determining lineages and genotypes of influenza A viruses.

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tagscomputational biology genetic databases genetic polymorphism genomics genotype influenza a virus orthomyxoviridae phylogeny viral genes viral genome viral proteins

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

OpenHUSARTool Content

http://genius.embnet.dkfz-heidelberg.de/menu/cgi-bin/w2h-open/w2h.open/w2h.start...

Protein > 2-D Structure Prediction
Protein > Domains and Motifs
Protein > Localization and Targeting
Sequence Comparison > Similarity Searching

Open HUSAR (Heidelberg Unix Sequence Analysis Resources) contains suite of bioinformatics pipelines including tasks oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep).

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tagsalgorithms computational biology protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

Pcons.netTool Content

http://pcons.net/

Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

Pcons.net is a protein structure prediction meta server that provides automated tools for protein structure prediction and analysis using a consensus approach.

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tagsalgorithms amino acid sequence animals automatic data processing automation computational biology computer simulation consensus sequence humans molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins roc curve secondary protein structure sensitivity and specificity sequence alignment statistical models tertiary protein structure

QSCOP - BLASTTool Content

http://qscop-blast.services.came.sbg.ac.at/

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

QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).

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tagsalgorithms amino acid sequence chemical models computational biology computer simulation molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins pyrococcus furiosus sequence alignment structure-activity relationship thermotoga maritima

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

WhETSTool Content

http://www.rothamsted.ac.uk/whets/

DNA > Sequence Polymorphisms
DNA > Sequence Retrieval and Submission
Model Organisms > Plants
Sequence Comparison > Similarity Searching

WhETS (Wheat Estimated Transcript Server) is a resource that combines Triticeae ESTs/mRNAs with rice genes to find the best estimate of hexaploid wheat transcript sequences for a target gene, supplemented with information on tissue distribution and likely gene structure, to aid in primer design.

This content is being maintained by RowanMitchell.

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tagscomputational biology expressed sequence tags genetic databases genetic models plant chromosomes plant genes plant genome ploidies sequence alignment single nucleotide polymorphism triticum

fastSCOPTool Content

http://gemdock.life.nctu.edu.tw/fastSCOP/

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

fastSCOP identifies structural domains and determines evolutionary superfamilies of a query protein structure using 3D-BLAST to scan SCOP and MAMMOTH to create a structural alignment for refining domain boundaries.

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tagsamino acid sequence amino acid sequence homology computational biology molecular evolution molecular models molecular sequence data protein conformation protein databases protein sequence analysis protein structural homology proteins statistical data interpretation tertiary protein structure

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins