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NAR Web Server Issue 2004

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DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

DNA > Annotations

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

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

DNA > DNA and Genomic Analysis

PlasMapperTool Content

http://wishart.biology.ualberta.ca/PlasMapper/index.html

DNA > DNA and Genomic Analysis
DNA > Tools For the Bench

Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats.

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tagschromosome mapping dna sequence analysis plasmids restriction mapping

WAViSTool Content

http://wavis.img.cas.cz/

DNA > DNA and Genomic Analysis
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.

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tagsdna sequence analysis humans protein sequence analysis rna sequence analysis sequence alignment sequence analysis

DNA > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

DNA > Gene Prediction

AGenDATool Content

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

DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

BLASTTool Content

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

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

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

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

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

DNA > Mapping and Assembly

PromoSerTool Content

http://biowulf.bu.edu/zlab/PromoSer/

DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection

Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.

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tagsalgorithms animals dna sequence analysis expressed sequence tags genetic promoter regions genome humans messenger rna mice oligonucleotide array sequence analysis rats rna sequence analysis sequence alignment sequence analysis transcription initiation site

DNA > Phylogeny Reconstruction

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

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

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

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

PDATool Content

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

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

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

This content is being maintained by soniacas.

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

PupaSuiteTool Content

http://pupasuite.bioinfo.cipf.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

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

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

SBT Interface - dbMHCTool Content

http://www.ncbi.nlm.nih.gov/gv/mhc/sbt.cgi?cmd=main

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

The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.

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tagsalgorithms alleles dna fingerprinting dna sequence analysis genetic polymorphism hla antigens immunologic receptors kir receptors nucleic acid databases sequence alignment
setsNational Center for Biotechnology Information (NCBI)

SNPboxTool Content

http://www.SNPbox.org

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms

Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.

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tagsdna primers exons genome nucleic acid databases polymerase chain reaction single nucleotide polymorphism

DNA > Sequence Retrieval and Submission

BLASTTool Content

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

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

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

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

PubCrawlerTool Content

http://pubcrawler.gen.tcd.ie/

DNA > Sequence Retrieval and Submission
Literature > Search Tools
Protein > Sequence Retrieval
RNA > Sequence Retrieval

It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).

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tagselectronic mail information services medline national library of medicine (u.s.) nucleic acid databases pubmed united states

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

NAR Database Issue 2010NAR Web Server Issue 2004
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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

DNA > Structure and Sequence Feature Detection

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

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

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/

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

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

CREMETool Content

http://creme.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources

CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.

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tagsbinding sites computational biology gene expression regulation genetic promoter regions human genome humans transcription factors

CSTminerTool Content

http://www.caspur.it/CSTminer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences

CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

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tagsanimals conserved sequence exons genomics humans intergenic dna mice nucleic acid regulatory sequences sequence tagged sites

CompareProspectorTool Content

http://compareprospector.stanford.edu/

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

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

ConsiteTool Content

http://www.phylofoot.org/consite/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

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tagsalgorithms animals binding sites computational biology conserved sequence dna dna footprinting dna sequence analysis genetic models human genome humans nucleic acid regulatory sequences phylogeny predictive value of tests regulator genes sensitivity and specificity sequence alignment transcription factors

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

IsoFinderTool Content

http://isofinder.sourceforge.net/

DNA > Structure and Sequence Feature Detection

IsoFinder is a tool for the prediction of isochores for a user-supplied sequence.

This content is being maintained by oliver.

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tagsalgorithms computational biology genomics isochores major histocompatibility complex

LowComplexityTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/

DNA > Structure and Sequence Feature Detection
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.

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tagsalgorithms bacterial genome chromosomes dna sequence analysis sequence alignment

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

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

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors

MoViESTool Content

http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl

DNA > Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design

MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.

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tagscomputational biology hydrogen bonding nucleic acids proteins thermodynamics vibration

MotifVizTool Content

http://biowulf.bu.edu/MotifViz/

DNA > Structure and Sequence Feature Detection

MotifViz is a tool for detecting overrepresented transcription factor binding motifs. Four motif discovery programs are accessible from the MotifViz web interface: Clover, Rover, Motifish and Possum.

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tagsalgorithms binding sites dna sequence analysis genetic promoter regions transcription factors

Onto-ToolsTool Content

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

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

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

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

POBOTool Content

http://ekhidna.biocenter.helsinki.fi/poxo/pobo/

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

POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.

This content is being maintained by mkankain.

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tagsarabidopsis binding sites computational biology dna sequence analysis gene expression regulation genetic promoter regions reproducibility of results transcription factors transcriptional regulatory elements

PredictRegulonTool Content

http://www.cdfd.org.in/predictregulon/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.

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

PromoSerTool Content

http://biowulf.bu.edu/zlab/PromoSer/

DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection

Server which aims to extract proximal promoter sequences from mammalian genomes. Does so by mapping mRNA and EST sequences and tracking overlapping alignments to find the transcription start site.

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tagsalgorithms animals dna sequence analysis expressed sequence tags genetic promoter regions genome humans messenger rna mice oligonucleotide array sequence analysis rats rna sequence analysis sequence alignment sequence analysis transcription initiation site

RECONTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/recon/

DNA > Structure and Sequence Feature Detection

RECON is a tool for calculating the probability of nucleosome formation along a DNA sequence input by the user.

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tagsalgorithms animals dna sequence analysis genetic promoter regions humans mice molecular sequence data nucleosomes

Rescue-ESETool Content

http://genes.mit.edu/burgelab/rescue-ese/

DNA > Structure and Sequence Feature Detection
Expression > Splicing

Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis exons genes human genome humans hypoxanthine phosphoribosyltransferase introns messenger rna mice nucleic acid databases nucleic acid regulatory sequences oligonucleotides point mutation ribonucleic acid regulatory sequences rna precursors rna sequence analysis rna splicing tetraodontiformes zebrafish

SITECONTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.

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tagsbinding sites dna dna sequence analysis nucleic acid conformation nucleic acid regulatory sequences sequence alignment transcription factors

SeqVISTATool Content

http://zlab.bu.edu/SeqVISTA/

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Alignment Editing and Visualization

Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister.

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tagsalgorithms amino acid sequence base sequence binding sites computational biology dna gene expression regulation genetic transcription humans molecular sequence data nucleic acid databases nucleic acid regulatory sequences sequence alignment simian virus 40 systems integration transcription factors viral genome

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

Web WeederTool Content

http://159.149.109.9/modtools/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.

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rVISTATool Content

http://rvista.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.

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DNA > Tools For the Bench

DEQORDatabase Content

http://deqor.mpi-cbg.de/deqor_new/input.html

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

Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.

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tagsrna interference small interfering rna

Electronic PCRDatabase Content

http://www.ncbi.nlm.nih.gov/sutils/e-pcr

DNA > Tools For the Bench

Find sequence-based markers (STSs) and therefore, map location in a DNA sequence of interest; useful for detecting mis-priming events.

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tagsalgorithms base sequence chromosome mapping computational biology dna primers dna sequence analysis factual databases human chromosomes humans molecular sequence data nucleic acid databases polymerase chain reaction sequence alignment sequence tagged sites

Gene2OligoTool Content

http://berry.engin.umich.edu/gene2oligo/

DNA > Tools For the Bench

Tool which divides both strands of an input DNA sequence into a set of contiguous oligonucleotides. These oligos are designed with complimentary regions so that the complete set can be combined to synthesize the input DNA sequence in vitro (using oligonucleotide synthesis and assembly PCR).

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tagsalgorithms cytochromes b5 dna ligases dna sequence analysis fungal genes nucleic acid hybridization oligonucleotides polymerase chain reaction saccharomyces cerevisiae temperature

PlasMapperTool Content

http://wishart.biology.ualberta.ca/PlasMapper/index.html

DNA > DNA and Genomic Analysis
DNA > Tools For the Bench

Web server that automatically generates and annotates circular plasmid maps. The tool has: a built in set of features that can be displayed (ie. RE sites, tags, ORFs, etc.); allows users to define custom features to display; contains a library of commonly used plasmids; and, generates nice looking images in a variety of output formats.

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tagschromosome mapping dna sequence analysis plasmids restriction mapping

ProbeLynxTool Content

http://www.pathogenomics.ca/probelynx

DNA > Tools For the Bench
Expression > Transcript Expression Analysis

Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.

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tagsanimals base sequence cattle chickens complementary dna dna probes gene expression profiling genomics humans messenger rna mice nucleic acid databases oligonucleotide array sequence analysis oligonucleotide probes

SNPboxTool Content

http://www.SNPbox.org

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms

Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.

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tagsdna primers exons genome nucleic acid databases polymerase chain reaction single nucleotide polymorphism

SfoldTool Content

http://sfold.wadsworth.org

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

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

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tagsalgorithms animals antisense oligonucleotides antisense rna base sequence bayes theorem binding sites catalytic rna computational biology drug design escherichia coli molecular sequence data nucleic acid conformation phylogeny probability protozoan rna rabbits ribosomal rna rna rna stability small interfering rna spliced leader rna statistical distributions statistical models tetrahymena thermophila thermodynamics transfer rna xenopus laevis

TRODTool Content

http://www.cellbio.unige.ch/RNAi.html

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

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

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tagscell line dna-directed rna polymerases double-stranded rna gene silencing green fluorescent proteins hela cells humans luminescent proteins messenger rna molecular cloning molecular sequence data oligodeoxyribonucleotides plasmids recombinant fusion proteins rna interference small interfering rna transfection viral proteins

siDirectTool Content

http://design.RNAi.jp/

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

Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.

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tagsalgorithms animals base sequence cell line chick embryo cricetinae drosophila gc rich sequence genetic models genetic vectors humans luciferases mammals mice molecular sequence data rna interference small interfering rna transfection

siRNA Selection ServerTool Content

http://jura.wi.mit.edu/bioc/siRNA

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

Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.

This content is being maintained by lewitter.

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tagsalgorithms animals humans mice oligonucleotides rna interference small interfering rna

Education > Community

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

Education > Directories and Portals

Bioinformatics Links DirectoryResource Content

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

Education > Directories and Portals

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

This content is being maintained by Francis Ouellette.

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

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

Expression > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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setsEuropean Bioinformatics Institute (EBI)

Expression > Gene Regulation

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

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

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

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BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/

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

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

CARRIETool Content

http://zlab.bu.edu/CARRIE-web

Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.

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tagsacquired immunodeficiency syndrome binding sites computational biology dna female gene expression profiling gene expression regulation genetic promoter regions genetic transcription hiv hiv infections humans male newborn infant nucleic acid regulatory sequences nurses oligonucleotide array sequence analysis physicians pregnancy transcription factors

CONFACTool Content

http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl

Expression > Gene Regulation
Expression > Transcript Expression Analysis

The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.

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tagsanimals binding sites ccaat-enhancer-binding protein-delta ccaat-enhancer-binding proteins dna sequence analysis gene expression profiling genetic promoter regions genomics humans male mice nf-kappa b oligonucleotide array sequence analysis prostatic neoplasms transcription factors

CREMETool Content

http://creme.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources

CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.

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tagsbinding sites computational biology gene expression regulation genetic promoter regions human genome humans transcription factors

CSTminerTool Content

http://www.caspur.it/CSTminer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences

CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

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tagsanimals conserved sequence exons genomics humans intergenic dna mice nucleic acid regulatory sequences sequence tagged sites

CompareProspectorTool Content

http://compareprospector.stanford.edu/

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

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

ConsiteTool Content

http://www.phylofoot.org/consite/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.

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tagsalgorithms animals binding sites computational biology conserved sequence dna dna footprinting dna sequence analysis genetic models human genome humans nucleic acid regulatory sequences phylogeny predictive value of tests regulator genes sensitivity and specificity sequence alignment transcription factors

DEQORDatabase Content

http://deqor.mpi-cbg.de/deqor_new/input.html

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

Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.

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IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

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

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors

Onto-ToolsTool Content

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

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

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

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

POBOTool Content

http://ekhidna.biocenter.helsinki.fi/poxo/pobo/

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

POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.

This content is being maintained by mkankain.

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tagsarabidopsis binding sites computational biology dna sequence analysis gene expression regulation genetic promoter regions reproducibility of results transcription factors transcriptional regulatory elements

PredictRegulonTool Content

http://www.cdfd.org.in/predictregulon/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.

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

Riboswitch finderTool Content

http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html

Expression > Gene Regulation
RNA > Motifs

RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.

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tagsallosteric regulation messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

SITECONTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/sitecon/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Server for the detection of conformational and physicochemical properties in transcription factor binding sites and potential binding sites.

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tagsbinding sites dna dna sequence analysis nucleic acid conformation nucleic acid regulatory sequences sequence alignment transcription factors

SfoldTool Content

http://sfold.wadsworth.org

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

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

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tagsalgorithms animals antisense oligonucleotides antisense rna base sequence bayes theorem binding sites catalytic rna computational biology drug design escherichia coli molecular sequence data nucleic acid conformation phylogeny probability protozoan rna rabbits ribosomal rna rna rna stability small interfering rna spliced leader rna statistical distributions statistical models tetrahymena thermophila thermodynamics transfer rna xenopus laevis

TRODTool Content

http://www.cellbio.unige.ch/RNAi.html

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

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

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tagscell line dna-directed rna polymerases double-stranded rna gene silencing green fluorescent proteins hela cells humans luminescent proteins messenger rna molecular cloning molecular sequence data oligodeoxyribonucleotides plasmids recombinant fusion proteins rna interference small interfering rna transfection viral proteins

Web WeederTool Content

http://159.149.109.9/modtools/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.

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tagsalgorithms binding sites computational biology dna gene expression regulation nucleic acid regulatory sequences transcription factors

rVISTATool Content

http://rvista.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Server which detects transcription factor binding sites(TFBS) through combining TFBS prediction, sequence comparison and cluster analysis.

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siDirectTool Content

http://design.RNAi.jp/

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

Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.

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tagsalgorithms animals base sequence cell line chick embryo cricetinae drosophila gc rich sequence genetic models genetic vectors humans luciferases mammals mice molecular sequence data rna interference small interfering rna transfection

siRNA Selection ServerTool Content

http://jura.wi.mit.edu/bioc/siRNA

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

Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.

This content is being maintained by lewitter.

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tagsalgorithms animals humans mice oligonucleotides rna interference small interfering rna

Expression > Protein Expression

ProMoSTTool Content

http://proteomics.mcw.edu/promost

Expression > Protein Expression
Protein > Biochemical Features
Protein > Protein Expression
Protein > Proteomics

ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.

This content is being maintained by halligan.

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tagsalgorithms gel electrophoresis isoelectric point molecular weight post-translational protein processing proteins

Expression > Splicing

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/

Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

Rescue-ESETool Content

http://genes.mit.edu/burgelab/rescue-ese/

DNA > Structure and Sequence Feature Detection
Expression > Splicing

Server for the identification of hexnucleotide exonic splicing enhancers (ESEs). Also contains a list of 238 identified ESEs for human genes.

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tagsanimals complementary dna computational biology consensus sequence dna sequence analysis exons genes human genome humans hypoxanthine phosphoribosyltransferase introns messenger rna mice nucleic acid databases nucleic acid regulatory sequences oligonucleotides point mutation ribonucleic acid regulatory sequences rna precursors rna sequence analysis rna splicing tetraodontiformes zebrafish

Expression > Transcript Expression Analysis

ArrayPipeTool Content

http://koch.pathogenomics.ca/cgi-bin/pub/arraypipe.pl

Expression > Transcript Expression Analysis

ArrayPipe allows users to customize a processing pipeline for the analysis of microarray data. Includes methods for quality assessment of slides, data visualization, normalization, and detection of differentially expressed genes. Output consists of reports formatted as standard web pages and tab-delimited lists of calculated values.

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tagsgene expression profiling oligonucleotide array sequence analysis

ArrayXPathTool Content

http://www.snubi.org/software/ArrayXPath/

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

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.

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tagscluster analysis gene expression profiling genetic databases genetic predisposition to disease medical subject headings oligonucleotide array sequence analysis signal transduction statistical data interpretation systems integration

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

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

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

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BioProspectorTool Content

http://robotics.stanford.edu/~xsliu/BioProspector/

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

Server which scans upstream of genes in the same gene expression cluster for regulatory sequence motifs using a Gibbs sampling strategy. The Markov background model is used for non-motif bases, improving specificity of predicted motif locations.

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tagsalgorithms bacillus subtilis base sequence binding sites carrier proteins conserved sequence cyclic amp receptor protein dna escherichia coli gene expression profiling gene expression regulation genetic models genetic transcription markov chains nucleic acid regulatory sequences oligonucleotide array sequence analysis rap1 gtp-binding proteins regulator genes saccharomyces cerevisiae sequence alignment tata box transcription factors

CARRIETool Content

http://zlab.bu.edu/CARRIE-web

Expression > Gene Regulation
Expression > Transcript Expression Analysis

Server which analyzes microarray and promoter sequence data associated with a response to a specific stimulus. After analysis a potential transcriptional regulatory network is created. CARRIE also determines which transcription factors were likely involved in regulation and which genes they regulated.

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tagsacquired immunodeficiency syndrome binding sites computational biology dna female gene expression profiling gene expression regulation genetic promoter regions genetic transcription hiv hiv infections humans male newborn infant nucleic acid regulatory sequences nurses oligonucleotide array sequence analysis physicians pregnancy transcription factors

CONFACTool Content

http://morenolab.whitehead.emory.edu/cgi-bin/confac/login.pl

Expression > Gene Regulation
Expression > Transcript Expression Analysis

The Conserved Transcription Factor Binding Site Finder (CONFAC) takes a list of human gene names and identifiers as input, and compares them with their mouse orthologues to identify conserved transcription factor binding sites. Further information from the user allows CONFAC to identify binding sites that are enriched in the promoter regions of gene clusters from microarray analyses when compared to control gene sets.

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tagsanimals binding sites ccaat-enhancer-binding protein-delta ccaat-enhancer-binding proteins dna sequence analysis gene expression profiling genetic promoter regions genomics humans male mice nf-kappa b oligonucleotide array sequence analysis prostatic neoplasms transcription factors

CompareProspectorTool Content

http://compareprospector.stanford.edu/

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

Server which attempts to identify any motifs related to genes predicted to share regulatory elements. It alters Gibbs sampling through biasing searches towards conserved sequences across multiple species.

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tagsalgorithms animals binding sites caenorhabditis caenorhabditis elegans conserved sequence dna eukaryotic cells fungal genes gene expression regulation genes genetic transcription genomics helminth genes humans mice nucleic acid regulatory sequences regulator genes saccharomyces saccharomyces cerevisiae schizosaccharomyces transcription factors

Expression ProfilerTool Content

http://www.ebi.ac.uk/expressionprofiler/

Expression > Transcript Expression Analysis

Expression Profiler is a web based platform for microarray data analysis developed at the EBI. This resource is integrated with the ArrayExpress database, a public repository for microarray data.

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tagsgene expression profiling genomics oligonucleotide array sequence analysis

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

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

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

GFINDerTool Content

http://www.medinfopoli.polimi.it/GFINDer/

Expression > Transcript Expression Analysis

Genome Functional INtegrated Discoverer (GFINDer) takes a list of gene/clone IDs with classification information as input, and allows the user to characterize the different gene classes in the list using annotations of various types from several different sources.

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tagscomputational biology controlled vocabulary gene expression profiling genetic databases genomics humans inborn genetic diseases oligonucleotide array sequence analysis phenotype proteins statistical data interpretation systems integration

KARMATool Content

http://biryani.med.yale.edu/karma/cgi-bin/mysql/karma.pl

Expression > Transcript Expression Analysis

KARMA (Keck Array Manager and Annotator) allows you compare and annotate your own microarrays against other available arrays. Comparison of arrays can be achieved within the same species as well as across species (array comparison is based on UniGene Cluster ID and/or Homologene data). Annotation data includes LocusLink, SwissProt, and Gene Ontology.

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tagsdna sequence analysis gene expression profiling oligonucleotide array sequence analysis

MDscanTool Content

http://robotics.stanford.edu/~xsliu/MDscan/

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

Server designed to pinpoint protein-DNA interaction sites at the base pair level. Uses ChIP-array data, word enumeration and position-specific weight matrix updating to search for motifs representing these interaction sites.

This content is being maintained by brutlag.

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tagsalgorithms base sequence binding sites chromatin computational biology dna dna-binding proteins fungal genes gene expression regulation genetic transcription nucleic acid regulatory sequences oligonucleotide array sequence analysis precipitin tests protein binding response elements saccharomyces cerevisiae saccharomyces cerevisiae proteins sensitivity and specificity telomere telomere-binding proteins time factors transcription factors

Onto-ToolsTool Content

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

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

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

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

POBOTool Content

http://ekhidna.biocenter.helsinki.fi/poxo/pobo/

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

POBO is a tool to summarize, verify and screen predetermined cis-element motifs from a set of sequences. POBO reports the results in as understandable format as possible for biologists.

This content is being maintained by mkankain.

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tagsarabidopsis binding sites computational biology dna sequence analysis gene expression regulation genetic promoter regions reproducibility of results transcription factors transcriptional regulatory elements

ProbeLynxTool Content

http://www.pathogenomics.ca/probelynx

DNA > Tools For the Bench
Expression > Transcript Expression Analysis

Using current releases of genomic sequence data, ProbeLynx allows users to assess the specificity of probe sequences used for microarray experiments. The user provides probe sequences in FASTA or tab-delimited format, and ProbeLynx reports specificity information for each probe and functional annotations from Ensembl or TIGR for each probe target hit.

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tagsanimals base sequence cattle chickens complementary dna dna probes gene expression profiling genomics humans messenger rna mice nucleic acid databases oligonucleotide array sequence analysis oligonucleotide probes

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

Expression > cDNA, EST, SAGE

E2GTool Content

http://bibiserv.techfak.uni-bielefeld.de/e2g/

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

E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.

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tagsbase sequence chromosome mapping complementary dna expressed sequence tags genomics sequence alignment

Human Genome > Annotations

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

Human Genome > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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setsEuropean Bioinformatics Institute (EBI)

Human Genome > Other Resources

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

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

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

CREMETool Content

http://creme.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Other Resources

CREME (Cis-Regulatory Module Explorer for the human genome) is a tool for identifying and visualizing cis-regulatory modules for a given set of genes that are potentially co-expressed or co-regulated. It takes as input a list of accession numbers, and reports back common modules, grouping genes from the list by which modules are found in their promoter regions.

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tagsbinding sites computational biology gene expression regulation genetic promoter regions human genome humans transcription factors

SBT Interface - dbMHCTool Content

http://www.ncbi.nlm.nih.gov/gv/mhc/sbt.cgi?cmd=main

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

The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.

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tagsalgorithms alleles dna fingerprinting dna sequence analysis genetic polymorphism hla antigens immunologic receptors kir receptors nucleic acid databases sequence alignment
setsNational Center for Biotechnology Information (NCBI)

Human Genome > Sequence Polymorphisms

PDATool Content

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

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

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

This content is being maintained by soniacas.

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

PupaSuiteTool Content

http://pupasuite.bioinfo.cipf.es

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

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

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

SBT Interface - dbMHCTool Content

http://www.ncbi.nlm.nih.gov/gv/mhc/sbt.cgi?cmd=main

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

The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.

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tagsalgorithms alleles dna fingerprinting dna sequence analysis genetic polymorphism hla antigens immunologic receptors kir receptors nucleic acid databases sequence alignment
setsNational Center for Biotechnology Information (NCBI)

SNPboxTool Content

http://www.SNPbox.org

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms

Tool for large-scale standardized primer design with specific modules for SNP and exon PCR amplification. Results are presented as HTML with genomic position, primer sequence, and PCR conditions. Precomputed SNPbox results for all Ensembl exons are also available on the server.

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tagsdna primers exons genome nucleic acid databases polymerase chain reaction single nucleotide polymorphism

Literature > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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setsEuropean Bioinformatics Institute (EBI)

Literature > Search Tools

PubCrawlerTool Content

http://pubcrawler.gen.tcd.ie/

DNA > Sequence Retrieval and Submission
Literature > Search Tools
Protein > Sequence Retrieval
RNA > Sequence Retrieval

It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).

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tagselectronic mail information services medline national library of medicine (u.s.) nucleic acid databases pubmed united states

Literature > Text Mining and Semantics

NLProtTool Content

http://cubic.bioc.columbia.edu/services/nlprot/index.html

Literature > Text Mining and Semantics
Protein > Sequence Retrieval

NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.

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tagsalgorithms amino acid sequence artificial intelligence protein databases publications pubmed terminology as topic

Model Organisms > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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setsEuropean Bioinformatics Institute (EBI)

Model Organisms > Fish

ECR BrowserTool Content

http://ecrbrowser.dcode.org/

Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

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Model Organisms > Fly

ECR BrowserTool Content

http://ecrbrowser.dcode.org/

Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

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Model Organisms > Microbes

CVTreeTool Content

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

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

Phydbac2Tool Content

http://igs-server.cnrs-mrs.fr/phydbac/

Model Organisms > Microbes
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.

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tagsartificial gene fusion bacterial chromosomes bacterial genes bacterial genome bacterial proteins chromosome mapping escherichia coli proteins genomics molecular evolution open reading frames phylogeny protein sequence analysis

Model Organisms > Mouse and Rat

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/

Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

BEARRTool Content

http://giscompute.gis.a-star.edu.sg/~vega/BEARR1.0/

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

Batch Extraction and Analysis of cis-Regulatory Regions (BEARR) takes a list of gene identifiers (such as RefSeq and Unigene IDs), consensus patterns, and (optionally) a position weight matrix as input and returns a list of matches for the patterns in both the sense and anti-sense strands of the relevant genomic sequence. The user specifies what distance up and downstream from both the transcription start site and the 3\' terminus to look for the patterns.

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tagsbinding sites dna dna sequence analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis software design transcription factors

ECR BrowserTool Content

http://ecrbrowser.dcode.org/

Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

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tagsanimals binding sites dna sequence analysis fishes genome genomics humans mice nucleic acid regulatory sequences rats sequence alignment synteny systems integration transcription factors

Model Organisms > Other Organisms

Genotyping - NCBITool Content

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Model Organisms > Other Organisms
Sequence Comparison > Other Alignment Tools

The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

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tagsalgorithms dna sequence analysis genetic recombination genotype hepacivirus hepatitis b virus hiv-1 molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

Model Organisms > Other Vertebrates

ECR BrowserTool Content

http://ecrbrowser.dcode.org/

Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

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tagsanimals binding sites dna sequence analysis fishes genome genomics humans mice nucleic acid regulatory sequences rats sequence alignment synteny systems integration transcription factors

Other Molecules > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

Protein > 2-D Structure Prediction

BOMPTool Content

http://www.bioinfo.no/tools/bomp

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

The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.

NAR Web Server Issue 2004
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tagsbacterial genome bacterial outer membrane proteins escherichia coli gram-negative bacteria protein sequence analysis salmonella typhimurium secondary protein structure

DICHROWEBTool Content

http://dichroweb.cryst.bbk.ac.uk/html/home.shtml

Protein > 2-D Structure Prediction

A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.

NAR Web Server Issue 2004
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tagsalgorithms circular dichroism computational biology protein databases secondary protein structure

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

Meta-BASICTool Content

http://basic.bioinfo.pl/

Protein > 2-D Structure Prediction
Sequence Comparison > Similarity Searching

Meta-BASIC is a tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.

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tagsalgorithms amino acid sequence homology glycosyltransferases molecular models protein sequence analysis protein structural homology proteins secondary protein structure sequence alignment trna methyltransferases

PRED-TMBBTool Content

http://bioinformatics.biol.uoa.gr/PRED-TMBB/

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

PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.

This content is being maintained by pbagos.

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tagsbacterial outer membrane proteins escherichia coli proteins gram-negative bacteria hidden markov model markov chains membrane proteins peptides predictive value of tests protein databases protein sequence analysis secondary protein structure statistical models tertiary protein structure topology prediction

PROSPECT-PSPPTool Content

http://csbl.bmb.uga.edu/protein_pipeline

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

An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses.

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tagscomputational biology genomics molecular models protein conformation protein sequence analysis proteins systems integration

PredictProteinTool Content

http://www.predictprotein.org

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

PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.

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tagsmolecular models protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins secondary protein structure sequence alignment systems integration tertiary protein structure time factors

STRIDETool Content

http://webclu.bio.wzw.tum.de/stride/

Protein > 2-D Structure Prediction

STRIDE takes a PDB structure as input and reports back either secondary structure assignments, a Ramachandran plot or a contact map.

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tagshydrogen bonding molecular structure protein databases proteins secondary protein structure

Protein > 3-D Structural Features

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/

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

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

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tagsamino acid motifs molecular models molecular structure proteins

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

COLORADO-3DTool Content

http://asia.genesilico.pl/colorado3d/

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

COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.

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tagsalgorithms amino acid sequence color conserved sequence molecular models protein conformation protein structural homology

FoldMiner and LOCK 2Tool Content

http://foldminer.stanford.edu/

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

FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.

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tagsalgorithms amino acid motifs molecular models protein conformation protein folding protein structural homology 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

PDBSiteScanTool Content

http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html

Protein > 3-D Structural Features

PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.

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tagsbinding sites catalytic domain hydrolases intracellular signaling peptides and proteins molecular models oncogene proteins post-translational protein processing proteins tertiary protein structure

SCitTool Content

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

Protein > 3-D Structural Features

SCit is a set of tools facilitating the analysis and editing of protein side chain conformations. Using a PDB file as input, the tools allow the user to perform such tasks as listing and/or modifying the values of the dihedral angles, listing structurally compatible rotamers for each residue and substituting side chains resulting in a new structure.

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tagsamino acids protein conformation proteins

iMOTTool Content

http://caps.ncbs.res.in/imot/iMOTserver.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.

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tagsamino acid motifs amino acid sequence homology protein databases protein folding protein sequence analysis protein tyrosine phosphatases

Protein > 3-D Structure Comparison

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/

Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

FATCATTool Content

http://fatcat.burnham.org/

Protein > 3-D Structure Comparison

FATCAT provides the means to compare two PDB-format protein structures, or to search for structures similar to a given PDB structure. The user can supply a PDB ID or upload a structure file. The FATCAT web server employs the Flexible structure AlignmenT by Chaining AFPs (Aligned Fragment Pairs) with Twists (FATCAT) algorithm.

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tagsalgorithms amino acid sequence amino acid sequence homology molecular sequence data protein databases protein sequence analysis protein structural homology proteins sequence alignment

FoldMiner and LOCK 2Tool Content

http://foldminer.stanford.edu/

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

FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.

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tagsalgorithms amino acid motifs molecular models protein conformation protein folding protein structural homology tertiary protein structure

ProteinDBSTool Content

http://proteindbs.rnet.missouri.edu/

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

ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time.

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tagsdatabase management systems molecular models protein conformation protein databases reproducibility of results tertiary protein structure time factors

SA-SearchTool Content

http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search

Protein > 3-D Structure Comparison

SA-Search is a tool which first converts a PDB structure file into a one-dimensional representation using a structural alphabet, and then searches for similarities using standard methods for sequence alignment.

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tagsamino acid sequence markov chains protein conformation protein structural homology sequence alignment

SuperPoseTool Content

http://wishart.biology.ualberta.ca/SuperPose/

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

SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules.

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tagsamino acid sequence protein databases protein structural homology sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

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

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

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

iMOTTool Content

http://caps.ncbs.res.in/imot/iMOTserver.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.

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tagsamino acid motifs amino acid sequence homology protein databases protein folding protein sequence analysis protein tyrosine phosphatases

Protein > 3-D Structure Prediction

COLORADO-3DTool Content

http://asia.genesilico.pl/colorado3d/

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

COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.

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tagsalgorithms amino acid sequence color conserved sequence molecular models protein conformation protein structural homology

CaspRTool Content

http://igs-server.cnrs-mrs.fr/Caspr/index.cgi

Protein > 3-D Structure Prediction

CaspR is a web tool for building structural models for protein sequences using molecular replacement and homology modelling. The software implements an automated approach that uses T-COFFEE to produce alignments, MODELLER to produce homology models, and finally uses AMoRe and CNS to produce the structural model.

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tagsescherichia coli proteins molecular models protein sequence analysis protein structural homology sequence alignment

PROSPECT-PSPPTool Content

http://csbl.bmb.uga.edu/protein_pipeline

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

An automated Protein Structure Prediction Pipeline (PSPP) based on multiple structure prediction tools. A key component of the pipeline is the fold recognition program, PROSPECT. Server supports genome scale analyses.

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tagscomputational biology genomics molecular models protein conformation protein sequence analysis proteins systems integration

PepBuildTool Content

http://www.imtech.res.in/bvs/pepbuild/

Protein > 3-D Structure Prediction

PepBuild is a tool that facilitates the construction, from known sequence and secondary/tertiary structures, of capped or uncapped proteins. The output generated is in PDB format.

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tagspeptides protein conformation protein databases proteins

RobettaTool Content

http://robetta.bakerlab.org/

Protein > 3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes

The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.

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tagsalanine biomolecular nuclear magnetic resonance molecular models protein conformation protein sequence analysis protein structural homology proteins reproducibility of results tertiary protein structure

SDPMODTool Content

http://proline.bic.nus.edu.sg/sdpmod/

Protein > 3-D Structure Prediction

SDPMOD is a comparative modelling tool for small disulfide-bonded proteins (SDPs).

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tagsconotoxins cysteine disulfides molecular models protein structural homology proteins reproducibility of results

WurstTool Content

http://www.zbh.uni-hamburg.de/wurst/

Protein > 3-D Structure Prediction

Wurst is a protein structure prediction tool that uses threading, aligning submitted sequences to thousands of PDB template structures.

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tagsamino acid substitution molecular models protein conformation protein sequence analysis

Protein > 3-D Structure Retrieval/Viewing

BSDDDatabase Content

http://iris.physics.iisc.ernet.in/bsdd/

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

BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

This content is being maintained by kitty.pillai.

NAR Web Server Issue 2004
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tagsamino acid motifs molecular models molecular structure proteins

CD-SearchDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

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

CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.

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tagsamino acid sequence animals consensus sequence conserved sequence molecular models protein databases protein sequence analysis proteins sequence alignment tertiary protein structure time factors

COLORADO-3DTool Content

http://asia.genesilico.pl/colorado3d/

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

COLORADO-3D allows you to color your protein structures to indicate the presence of potential errors in protein structure (detected by ANOLEA, PROSAII, PROVE or VERIFY3D), buried residues, and sequence conservation. The server returns a PDB-formatted file which can be displayed in RASMOL.

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tagsalgorithms amino acid sequence color conserved sequence molecular models protein conformation protein structural homology

ElNemoTool Content

http://igs-server.cnrs-mrs.fr/elnemo/start.html

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

ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.

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tagsmolecular models motion protein conformation proteins x-ray crystallography

MONSTERTool Content

http://monster.northwestern.edu/

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

MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.

This content is being maintained by samseaver.

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tagsmacromolecular substances molecular structure nucleic acids peptides proteins

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

ProteinDBSTool Content

http://proteindbs.rnet.missouri.edu/

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

ProteinDBS takes a PDB ID or structure as input, and searches for similar protein tertiary structures using computer visualization techniques. The superposition of structures and the aligned component of the sequence can then be viewed over the web. ProteinDBS v2.0 applies advanced feature extraction algorithms and scalable indexing techniques to achieve a fast computation time.

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tagsdatabase management systems molecular models protein conformation protein databases reproducibility of results tertiary protein structure time factors

SuperPoseTool Content

http://wishart.biology.ualberta.ca/SuperPose/

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

SuperPose is a tool for superpositions of protein structures. SuperPose generates sequence alignments, structure alignments, PDB coordinates and RMSD statistics, difference distance plots, and images of the superimposed molecules.

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tagsamino acid sequence protein databases protein structural homology sequence alignment

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

Protein > Annotation and Function

GObletTool Content

http://goblet.molgen.mpg.de/

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

GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.

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tagsanimals complementary dna dna sequence analysis genes humans invertebrates mice plants protein databases protein sequence analysis proteins reproducibility of results sequence homology terminology as topic

GPCRpredTool Content

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

Protein > Annotation and Function

GPCRpred is a tool that uses a support vector machine based method to make GPCR family and subfamily predictions for a user-supplied query sequence.

This content is being maintained by raghavagps.

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tagsartificial intelligence dipeptides g-protein-coupled receptors protein sequence analysis reproducibility of results

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

LOCtargetTool Content

http://www.rostlab.org/services/LOCtarget/

Protein > Annotation and Function

LOCtarget is a tool for predicting, and a database of pre-computed predictions for, sub-cellular localization of eukaryotic and prokaryotic proteins. Several methods are employed to make the predictions, including text analysis of SWISS-PROT keywords, nuclear localization signals, and the use of neural networks.

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tagsamino acid sequence homology eukaryotic cells genetic databases genomics neural networks (computer) nuclear localization signals prokaryotic cells protein sequence analysis protein sorting signals proteins

MITOPREDTool Content

http://bioinformatics.albany.edu/~mitopred/

Protein > Annotation and Function

MITOPRED uses Pfam domains, pI values and amino acid composition to predict nuclear-encoded mitochondrial proteins. Predictions have been precomputed for a number of proteomes, as well as for all Eukaryotic sequences in Swiss-Prot and TrEMBL. Users may directly enter or upload a file with a list of protein sequences or Swiss-Prot/TrEMBL accession numbers.

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tagsalgorithms animals cell nucleus gene expression profiling genome humans mitochondrial proteins protein databases protein sequence analysis proteome reproducibility of results sensitivity and specificity sequence alignment software design tertiary protein structure tissue distribution

MoViESTool Content

http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl

DNA > Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design

MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.

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tagscomputational biology hydrogen bonding nucleic acids proteins thermodynamics vibration

PRED-GPCRTool Content

http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/

Protein > Annotation and Function
Protein > Domains and Motifs

PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.

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tagsg-protein-coupled receptors protein sequence analysis reproducibility of results

Phydbac2Tool Content

http://igs-server.cnrs-mrs.fr/phydbac/

Model Organisms > Microbes
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.

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tagsartificial gene fusion bacterial chromosomes bacterial genes bacterial genome bacterial proteins chromosome mapping escherichia coli proteins genomics molecular evolution open reading frames phylogeny protein sequence analysis

PrediSiTool Content

http://www.predisi.de/

Protein > Annotation and Function
Protein > Localization and Targeting

PrediSi (Prediction of Signal Peptides) takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome datasets.

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tagsbacterial proteins eukaryotic cells peptides protein sequence analysis protein sorting signals proteome reproducibility of results

Proteome AnalystTool Content

http://www.cs.ualberta.ca/~bioinfo/PA/

Protein > Annotation and Function
Protein > Proteomics

Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers.

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tagsprotein sequence analysis proteins proteome proteomics reproducibility of results

SDPpredTool Content

http://bioinf.fbb.msu.ru/SDPpred/

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

SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences.

This content is being maintained by okalinina.

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tagsalgorithms amino acid sequence homology amino acids molecular models protein sequence analysis proteins sequence alignment

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

Protein > Biochemical Features

GDAPTool Content

http://www.doe-mbi.ucla.edu/Services/GDAP

Protein > Biochemical Features
Protein > Sequence Features

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.

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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins cysteine disulfides protein sequence analysis statistical data interpretation

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

MONSTERTool Content

http://monster.northwestern.edu/

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

MONSTER takes a PDB structure file as input, and predicts non-bonding interactions that have the potential to provide stability to the molecule. The output can be viewed or downloaded as XML or text, or can be viewed as a 3D structure or a 2D diagram. There is also a good tutorial available at the site.

This content is being maintained by samseaver.

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tagsmacromolecular substances molecular structure nucleic acids peptides 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

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

ProMoSTTool Content

http://proteomics.mcw.edu/promost

Expression > Protein Expression
Protein > Biochemical Features
Protein > Protein Expression
Protein > Proteomics

ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.

This content is being maintained by halligan.

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tagsalgorithms gel electrophoresis isoelectric point molecular weight post-translational protein processing proteins

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

QgridTool Content

http://www.netasa.org/qgrid/index.html

Protein > Biochemical Features

Server which provides cluster tree diagrams of a protein based on the charged atoms or hydrophobicity of each of its residues. The diagram allows for visual inspection of the distribution of hydrophobic and charged regions in proteins.

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tagshydrophobic and hydrophilic interactions ions proteins

Protein > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

Protein > Domains and Motifs

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

CD-SearchDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

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

CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.

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tagsamino acid sequence animals consensus sequence conserved sequence molecular models protein databases protein sequence analysis proteins sequence alignment tertiary protein structure time factors

CHOPTool Content

http://www.rostlab.org/services/CHOP/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.

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tagsalgorithms amino acid sequence homology protein sequence analysis proteomics tertiary protein structure

FoldMiner and LOCK 2Tool Content

http://foldminer.stanford.edu/

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

FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.

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tagsalgorithms amino acid motifs molecular models protein conformation protein folding protein structural homology tertiary protein structure

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

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

NRPS-PKSTool Content

http://www.nii.res.in/nrps-pks.html

Protein > Domains and Motifs

NRPS-PKS is an tool comprising four integrated databases for the analysis of large multi-enzymatic multi-domain megasynthases. The user can submit a query sequence to search for domains or view the properties of the products.

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tagsmultienzyme complexes peptide synthases protein databases substrate specificity tertiary protein structure

PRED-GPCRTool Content

http://athina.biol.uoa.gr/bioinformatics/PRED-GPCR/

Protein > Annotation and Function
Protein > Domains and Motifs

PRED-GPCR is a tool which queries user-supplied sequences against a database of HMMs corresponding to G-protein coupled receptor (GPCR) families in order to determine which GPCR family the query sequence most resembles.

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tagsg-protein-coupled receptors protein sequence analysis reproducibility of results

PredictProteinTool Content

http://www.predictprotein.org

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

PredictProtein is a protein sequence analysis and structure prediction tool. Users provide a protein sequence, and PredictProtein reports similar sequences, PROSITE sequence motifs, and various types of structure prediction information. You can also use META PredictProtein to submit a sequence to one web form and query several other servers at once, retrieving the results by e-mail.

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tagsmolecular models protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins secondary protein structure sequence alignment systems integration tertiary protein structure time factors

SledgeHMMERTool Content

http://bioapps.rit.albany.edu/sledgeHMMER/

Protein > Domains and Motifs

SledgeHMMER is a tool for searching the Pfam database using a parallelized version of the program hmmpfam. The user can perform queries with one or more sequences at a time and then receive the results by e-mail.

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tagsalgorithms protein databases protein sequence analysis software design tertiary protein structure

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

iMOTTool Content

http://caps.ncbs.res.in/imot/iMOTserver.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.

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tagsamino acid motifs amino acid sequence homology protein databases protein folding protein sequence analysis protein tyrosine phosphatases

Protein > Interactions, Pathways, Enzymes

ArrayXPathTool Content

http://www.snubi.org/software/ArrayXPath/

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

ArrayXPath is a web-based service for matching microarray gene-expression profiles with known biological pathways. Input is a clustered gene-expression profile in a tab-delimited text format. Output includes pathway diagrams.

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tagscluster analysis gene expression profiling genetic databases genetic predisposition to disease medical subject headings oligonucleotide array sequence analysis signal transduction statistical data interpretation systems integration

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

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

PathBLASTTool Content

http://www.pathblast.org/

Protein > Interactions, Pathways, Enzymes

PathBLAST is a tool for cross-species comparison of protein interaction networks. PathBLAST takes a short protein interaction path as input and searches against an available protein-protein interation network specified by the user.

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tagsanimals protein interaction mapping protein sequence analysis signal transduction

RobettaTool Content

http://robetta.bakerlab.org/

Protein > 3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes

The Robetta server provides protein structure prediction tools and interface alanine scanning. The structure prediction is accomplished by either comparative modelling or the de novo Rosetta fragment insertion method. Interface alanine scanning is employed to predict how protein-protein interactions could be affected by mutations.

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tagsalanine biomolecular nuclear magnetic resonance molecular models protein conformation protein sequence analysis protein structural homology proteins reproducibility of results tertiary protein structure

SBT Interface - dbMHCTool Content

http://www.ncbi.nlm.nih.gov/gv/mhc/sbt.cgi?cmd=main

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

The SBT (Sequencing-based typing) interface is a tool accompanying the NCBI's Major Histocompatibility Complex database (dbMHC). It identifies the allelic composition of sequence-based typing (SBT) results of cDNA or genomic sequences. Samples are compared with databases containing all known alleles for several human leukocyte antigen (HLA) and killer cell immunoglobulin-like receptors (KIR) loci. An interactive sequence viewer allows inspection of the alignments.

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tagsalgorithms alleles dna fingerprinting dna sequence analysis genetic polymorphism hla antigens immunologic receptors kir receptors nucleic acid databases sequence alignment
setsNational Center for Biotechnology Information (NCBI)

WebInterViewerTool Content

http://interviewer.inha.ac.kr/

Protein > Interactions, Pathways, Enzymes

WebInterViewer is a tool for visualizing molecular interaction networks. It employs a fast-layout algorithm, and can visualize data from interaction databases directly.

This content is being maintained by khan.

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tagsmacromolecular substances protein interaction mapping

iMOTTool Content

http://caps.ncbs.res.in/imot/iMOTserver.html

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.

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tagsamino acid motifs amino acid sequence homology protein databases protein folding protein sequence analysis protein tyrosine phosphatases

Protein > Localization and Targeting

BOMPTool Content

http://www.bioinfo.no/tools/bomp

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

The beta-barrel Outer Membrane protein Predictor (BOMP) takes one or more fasta-formatted polypeptide sequences from Gram-negative bacteria as input and predicts whether or not they are beta-barrel integral outer membrane proteins.

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tagsbacterial genome bacterial outer membrane proteins escherichia coli gram-negative bacteria protein sequence analysis salmonella typhimurium secondary protein structure

ESLpredTool Content

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

Protein > Localization and Targeting

ESLpred is a tool for predicting subcellular localization of proteins using support vector machines. The predictions are based on dipeptide and amino acid composition, and physico-chemical properties.

This content is being maintained by raghavagps.

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tagsartificial intelligence dipeptides eukaryotic cells protein databases proteins reproducibility of results

PRED-TMBBTool Content

http://bioinformatics.biol.uoa.gr/PRED-TMBB/

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

PRED-TMBB is a tool that takes a Gram-negative bacteria protein sequence as input and predicts the transmembrane strands and the probability of it being an outer membrane beta-barrel protein. The user has a choice of three different decoding methods.

This content is being maintained by pbagos.

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tagsbacterial outer membrane proteins escherichia coli proteins gram-negative bacteria hidden markov model markov chains membrane proteins peptides predictive value of tests protein databases protein sequence analysis secondary protein structure statistical models tertiary protein structure topology prediction

PrediSiTool Content

http://www.predisi.de/

Protein > Annotation and Function
Protein > Localization and Targeting

PrediSi (Prediction of Signal Peptides) takes one or more amino acid sequences as input and predicts the likelihood that they are signal peptides as well as their cleavage positions. It can be used to analyse whole proteome datasets.

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tagsbacterial proteins eukaryotic cells peptides protein sequence analysis protein sorting signals proteome reproducibility of results

Protein > Molecular Dynamics and Docking

BioInfo3DTool Content

http://bioinfo3d.cs.tau.ac.il/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Interactions, Pathways, Enzymes
Protein > Molecular Dynamics and Docking

BioInfo3D is a collection of tools for the structural analysis of proteins, including tools for structural alignments and prediction of protein interactions.

This content is being maintained by BioInfo3D.

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tagsalgorithms computational biology ligands macromolecular substances protein conformation proteins secondary protein structure

ClusProTool Content

http://cluspro.bu.edu/login.php

Protein > Molecular Dynamics and Docking

ClusPro is a tool for automatically computing the docking of two protein structures supplied by the user (or as PDB IDs). The result set is a ranked list of putative complexes, ordered by clustering properties.

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tagsalgorithms antibodies antigens binding sites biological models chemical models cluster analysis computational biology discriminant analysis energy transfer enzyme inhibitors fourier analysis molecular dynamics simulation molecular models monte carlo method protein binding protein conformation protein interaction mapping protein multimerization proteins reproducibility of results sensitivity and specificity static electricity time factors

ElNemoTool Content

http://igs-server.cnrs-mrs.fr/elnemo/start.html

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

ElNemo (The Elastic Network Model) is a tool for predicting the possible movements (ie. conformational changes and other structural changes) of macromolecules. This tool allows users to compute, visualize, and analyse low-frequency normal modes of a protein.

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tagsmolecular models motion protein conformation proteins x-ray crystallography

MoViESTool Content

http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl

DNA > Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design

MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.

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tagscomputational biology hydrogen bonding nucleic acids proteins thermodynamics vibration

Protein > Phylogeny Reconstruction

CVTreeTool Content

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

Model Organisms > Microbes
Protein > Phylogeny Reconstruction

Composition Vector Tree (CVTree) infers phylogenetic relationships between microbial organisms by comparing their proteomes using a composition vector approach.

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tagsalgorithms archaeal genome bacteria bacterial genome chloroplast dna fungal genome genome genomics phylogeny viral genome viruses

Phydbac2Tool Content

http://igs-server.cnrs-mrs.fr/phydbac/

Model Organisms > Microbes
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.

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tagsartificial gene fusion bacterial chromosomes bacterial genes bacterial genome bacterial proteins chromosome mapping escherichia coli proteins genomics molecular evolution open reading frames phylogeny protein sequence analysis

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

WAViSTool Content

http://wavis.img.cas.cz/

DNA > DNA and Genomic Analysis
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.

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tagsdna sequence analysis humans protein sequence analysis rna sequence analysis sequence alignment sequence analysis

Protein > Protein Expression

ProMoSTTool Content

http://proteomics.mcw.edu/promost

Expression > Protein Expression
Protein > Biochemical Features
Protein > Protein Expression
Protein > Proteomics

ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.

This content is being maintained by halligan.

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tagsalgorithms gel electrophoresis isoelectric point molecular weight post-translational protein processing proteins

Protein > Proteomics

ISOTOPICATool Content

http://coco.protein.osaka-u.ac.jp/isotopica/

Protein > Proteomics

Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptides/proteins, DNA/RNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.

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tagsamino acid sequence base sequence biopolymers carbohydrate sequence ions isotopes mass spectrometry mathematical computing peptide mapping

ProMoSTTool Content

http://proteomics.mcw.edu/promost

Expression > Protein Expression
Protein > Biochemical Features
Protein > Protein Expression
Protein > Proteomics

ProMoST (Protein Modification Screening Tool) is a program to calculate accurate MW and pI values from proteins considering the effects of post-translational modifications. Results are displayed as calculated values of pI and MW for each protein and are also plotted on two-dimensional (2D) gel images.

This content is being maintained by halligan.

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tagsalgorithms gel electrophoresis isoelectric point molecular weight post-translational protein processing proteins

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

Proteome AnalystTool Content

http://www.cs.ualberta.ca/~bioinfo/PA/

Protein > Annotation and Function
Protein > Proteomics

Proteome Analyst is a high-throughput tool for predicting properties for each protein in a proteome. The user provides a proteome in fasta format, and the system employs Psi-blast, Psipred and Modeller to predict protein function and subcellular localization. Proteome Analyst uses machine-learned classifiers to predict things such as GO molecular function. User-supplied training data can also be used to create custom classifiers.

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tagsprotein sequence analysis proteins proteome proteomics reproducibility of results

Protein > Sequence Features

GDAPTool Content

http://www.doe-mbi.ucla.edu/Services/GDAP

Protein > Biochemical Features
Protein > Sequence Features

The Genomic Disulfide Analysis Program (GDAP) predicts disulfide bonds for a user-supplied protein sequence. GDAP also provides access to pre-computed predictions of disulfide bonds for over 100 microbial genomes.

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tagsarchaeal genome archaeal proteins bacterial genome bacterial proteins cysteine disulfides protein sequence analysis statistical data interpretation

LowComplexityTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/

DNA > Structure and Sequence Feature Detection
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.

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tagsalgorithms bacterial genome chromosomes dna sequence analysis sequence alignment

Protein > Sequence Retrieval

BLASTTool Content

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

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

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

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

NLProtTool Content

http://cubic.bioc.columbia.edu/services/nlprot/index.html

Literature > Text Mining and Semantics
Protein > Sequence Retrieval

NLProt is a tool for finding protein names in natural language text. This data-mining method is a useful approach for extracting protein UniprotIDs from research articles for the construction of custom datasets and/or databases.

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tagsalgorithms amino acid sequence artificial intelligence protein databases publications pubmed terminology as topic

PubCrawlerTool Content

http://pubcrawler.gen.tcd.ie/

DNA > Sequence Retrieval and Submission
Literature > Search Tools
Protein > Sequence Retrieval
RNA > Sequence Retrieval

It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).

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tagselectronic mail information services medline national library of medicine (u.s.) nucleic acid databases pubmed united states

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

RNA > Databases

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

RNA > Motifs

ERPINTool Content

http://tagc.univ-mrs.fr/erpin/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

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tagsalgorithms base sequence computational biology conserved sequence gene expression regulation iron nucleic acid conformation nucleic acid sequence homology response elements ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis selenocysteine sensitivity and specificity sequence alignment transfer rna

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

Riboswitch finderTool Content

http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html

Expression > Gene Regulation
RNA > Motifs

RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.

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tagsallosteric regulation messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

RNA > Sequence Retrieval

BLASTTool Content

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

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

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

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

PubCrawlerTool Content

http://pubcrawler.gen.tcd.ie/

DNA > Sequence Retrieval and Submission
Literature > Search Tools
Protein > Sequence Retrieval
RNA > Sequence Retrieval

It goes to the library. You go to the pub; receive email alerts for current contents of PubMed and GenBank; e.g. use accession number of htg record as query to receive sequence updates (as the version number changes).

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tagselectronic mail information services medline national library of medicine (u.s.) nucleic acid databases pubmed united states

RNA > Structure Prediction, Visualization, and Design

CARNACTool Content

http://bioinfo.lifl.fr/carnac

RNA > Structure Prediction, Visualization, and Design

Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned.

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tagsalgorithms catalytic rna cytochromes endoribonucleases enterovirus genetic models messenger rna molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology ribonuclease p ribosomal rna rna rna sequence analysis sequence alignment statistical models telomerase viral rna

DEQORDatabase Content

http://deqor.mpi-cbg.de/deqor_new/input.html

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

Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high silencing capacity.

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tagsrna interference small interfering rna

ERPINTool Content

http://tagc.univ-mrs.fr/erpin/

RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and others) in your sequence(s) of interest. Also contains tool for drawing secondary structure of motifs.

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tagsalgorithms base sequence computational biology conserved sequence gene expression regulation iron nucleic acid conformation nucleic acid sequence homology response elements ribonucleic acid regulatory sequences ribosomal rna rna rna sequence analysis selenocysteine sensitivity and specificity sequence alignment transfer rna

ILMTool Content

http://cic.cs.wustl.edu/RNA/

RNA > Structure Prediction, Visualization, and Design

Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or individual sequences.

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tagsalgorithms bacillus subtilis bacterial rna base composition base pairing base sequence escherichia coli feedback molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology phylogeny reproducibility of results rna rna sequence analysis sensitivity and specificity sequence alignment theoretical models thermodynamics transfer rna

MoViESTool Content

http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl

DNA > Structure and Sequence Feature Detection
Protein > Annotation and Function
Protein > Molecular Dynamics and Docking
RNA > Structure Prediction, Visualization, and Design

MoViES (Molecular Vibrations Evaluation Server) allows the computation of the vibrational and thermal fluctuations dynamics for the chemical bonds of biomolecules. The server takes as input a structure file in PDB format and returns results by email. Analysis of vibrational motions and thermal fluctuational dynamics can give insights into the functional properties of both proteins and nucleic acids.

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tagscomputational biology hydrogen bonding nucleic acids proteins thermodynamics vibration

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

SfoldTool Content

http://sfold.wadsworth.org

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

Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features.

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tagsalgorithms animals antisense oligonucleotides antisense rna base sequence bayes theorem binding sites catalytic rna computational biology drug design escherichia coli molecular sequence data nucleic acid conformation phylogeny probability protozoan rna rabbits ribosomal rna rna rna stability small interfering rna spliced leader rna statistical distributions statistical models tetrahymena thermophila thermodynamics transfer rna xenopus laevis

TRODTool Content

http://www.cellbio.unige.ch/RNAi.html

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

T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering.

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tagscell line dna-directed rna polymerases double-stranded rna gene silencing green fluorescent proteins hela cells humans luminescent proteins messenger rna molecular cloning molecular sequence data oligodeoxyribonucleotides plasmids recombinant fusion proteins rna interference small interfering rna transfection viral proteins

siDirectTool Content

http://design.RNAi.jp/

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

Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates.

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tagsalgorithms animals base sequence cell line chick embryo cricetinae drosophila gc rich sequence genetic models genetic vectors humans luciferases mammals mice molecular sequence data rna interference small interfering rna transfection

siRNA Selection ServerTool Content

http://jura.wi.mit.edu/bioc/siRNA

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

Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of a potential siRNA.

This content is being maintained by lewitter.

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tagsalgorithms animals humans mice oligonucleotides rna interference small interfering rna

Sequence Comparison > Alignment Editing and Visualization

CHAOS/DIALIGN WWW serverTool Content

http://dialign.gobics.de/chaos-dialign-submission

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.

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tagsalgorithms animals chickens computational biology dna sequence analysis genome genomics humans leukemia mice neoplasm dna neoplasm genes nucleic acid regulatory sequences rats sensitivity and specificity sequence alignment software validation stem cells tetraodontiformes zebrafish

SeqVISTATool Content

http://zlab.bu.edu/SeqVISTA/

DNA > Structure and Sequence Feature Detection
Sequence Comparison > Alignment Editing and Visualization

Tool for sequence feature visualization and comparison; integrates with Internet Explorer; accepts GenBank Flat Files, GenBank HTML, FASTA files; plugins exist for visualization of output from RepeatMasker, PsiPred, and Cister.

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tagsalgorithms amino acid sequence base sequence binding sites computational biology dna gene expression regulation genetic transcription humans molecular sequence data nucleic acid databases nucleic acid regulatory sequences sequence alignment simian virus 40 systems integration transcription factors viral genome

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

WAViSTool Content

http://wavis.img.cas.cz/

DNA > DNA and Genomic Analysis
Protein > Presentation and Format
Sequence Comparison > Alignment Editing and Visualization

The Web Alignment Visualization Server (WAViS) provides various web tools to enhance the presentation of amino acid or nucleotide multiple sequence alignments.

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tagsdna sequence analysis humans protein sequence analysis rna sequence analysis sequence alignment sequence analysis

Sequence Comparison > Analysis of Aligned Sequences

AGenDATool Content

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

DNA > Gene Prediction
Sequence Comparison > Analysis of Aligned Sequences

AGenDA is a web tool that compares the genomic sequences from evolutionarily related organisms in order to make gene predictions. It takes pairs of genomic sequences as input, aligns the sequences, and makes predictions based on splice signals, start and stop codons, and areas of conserved sequence.

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tagsanimals base sequence conserved sequence dna footprinting dna sequence analysis genes genomics humans mice nucleic acid sequence homology phylogeny rna splicing sequence alignment

ASmodelerTool Content

http://genome.ewha.ac.kr/ECgene/ASmodeler/

Expression > Splicing
Model Organisms > Mouse and Rat
Sequence Comparison > Analysis of Aligned Sequences

Gene modeling server which focuses on the modeling of alternative splicing. It is based on the alignment of mRNA, EST and protein sequences and combines genome-based clustering and transcript assembly. Supports human, mouse and rat genomes.

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tagsalgorithms alternative splicing animals exons expressed sequence tags genetic models genome humans messenger rna mice molecular sequence data protein sequence analysis rats rna sequence analysis sequence alignment

CRASPTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/

Sequence Comparison > Analysis of Aligned Sequences

Correlation analysis of the amino acid substitutions in protein sequences (CRASP) takes multiple alignments of amino acid sequences as input, and detects coordinated residue substitutions. These substitutions may suggest dependent evolution of functionally related pairs of amino acids.

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tagsamino acid substitution protein sequence analysis sequence alignment

CSTminerTool Content

http://www.caspur.it/CSTminer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Sequence Comparison > Analysis of Aligned Sequences

CSTminer searches for Conserved Sequence Tags (CST) in pairwise comparisons of genomic sequences. Output is a graphical map showing the location of CSTs overlayed with known Ensembl exons and ESTs. A scoring system reflects coding or non-coding potential of these conserved blocks.

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tagsanimals conserved sequence exons genomics humans intergenic dna mice nucleic acid regulatory sequences sequence tagged sites

ECR BrowserTool Content

http://ecrbrowser.dcode.org/

Model Organisms > Fish
Model Organisms > Fly
Model Organisms > Mouse and Rat
Model Organisms > Other Vertebrates
Sequence Comparison > Analysis of Aligned Sequences

The ECR (Evolutionary Conserved Regions) browser is a web-based tool for visualizing and navigating through whole genome alignments of several vertebrate species. Users can also submit sequences for alignment with one of the genomes represented.

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tagsanimals binding sites dna sequence analysis fishes genome genomics humans mice nucleic acid regulatory sequences rats sequence alignment synteny systems integration transcription factors

GObletTool Content

http://goblet.molgen.mpg.de/

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

GOblet allows the user to BLAST one or more protein or nucleotide sequences against databases that have sequences mapped to Gene Ontology (GO) terms. Results can be viewed for individual sequences, or as survey statistics for the group if more than one sequence is submitted.

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tagsanimals complementary dna dna sequence analysis genes humans invertebrates mice plants protein databases protein sequence analysis proteins reproducibility of results sequence homology terminology as topic

LowComplexityTool Content

http://wwwmgs.bionet.nsc.ru/mgs/programs/low_complexity/

DNA > Structure and Sequence Feature Detection
Protein > Sequence Features
Sequence Comparison > Analysis of Aligned Sequences

LowComplexity is a tool that searches for low complexity regions of DNA or protein sequences. Using LowComplexity you can search long sequences (chromosomes, genomes) or a set of aligned sequences. This resource also contains links to other algorithms for evaluating the complexity of sequences.

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tagsalgorithms bacterial genome chromosomes dna sequence analysis sequence alignment

PDATool Content

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

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

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

This content is being maintained by soniacas.

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

Phydbac2Tool Content

http://igs-server.cnrs-mrs.fr/phydbac/

Model Organisms > Microbes
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.

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tagsartificial gene fusion bacterial chromosomes bacterial genes bacterial genome bacterial proteins chromosome mapping escherichia coli proteins genomics molecular evolution open reading frames phylogeny protein sequence analysis

SDPpredTool Content

http://bioinf.fbb.msu.ru/SDPpred/

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

SDPpred is a tool for predicting which residues of a protein determine functional differences relative to its homologues. It takes as input an multiple sequence alignment of a protein family divided into groups based on the perceived functional differences.

This content is being maintained by okalinina.

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tagsalgorithms amino acid sequence homology amino acids molecular models protein sequence analysis proteins sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

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

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

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

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 > Comparative Genomics

Phydbac2Tool Content

http://igs-server.cnrs-mrs.fr/phydbac/

Model Organisms > Microbes
Protein > Annotation and Function
Protein > Phylogeny Reconstruction
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Comparative Genomics

Phydbac2 (Phylogenomic display of bacterial genes) is a tool to visualize and explore the phylogenomic profiles of bacterial protein sequences. It also allows the user to view sequence similarity across different organisms, access other genes with similar conservation profiles, and view genes that are found nearby a selected gene in multiple genomes.

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tagsartificial gene fusion bacterial chromosomes bacterial genes bacterial genome bacterial proteins chromosome mapping escherichia coli proteins genomics molecular evolution open reading frames phylogeny protein sequence analysis

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

CE-MCTool Content

http://bioinformatics.albany.edu/~cemc/

Protein > 3-D Structure Comparison
Sequence Comparison > Multiple Sequence Alignments

A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.

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tagsalgorithms amino acid sequence amino acid sequence homology aspartic acid endopeptidases factual databases molecular sequence data monte carlo method protein kinases proteins secondary protein structure sequence alignment software design

CHAOS/DIALIGN WWW serverTool Content

http://dialign.gobics.de/chaos-dialign-submission

Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Multiple Sequence Alignments

The CHAOS/DIALIGN WWW server is a multiple sequence alignment site which passes input sequences through CHAOS to create a list of local similarites. These similarities serve as anchor points, allowing DIALIGN to conduct global alignments faster. ABC can then be used for the interactive visualization of the alignment.

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tagsalgorithms animals chickens computational biology dna sequence analysis genome genomics humans leukemia mice neoplasm dna neoplasm genes nucleic acid regulatory sequences rats sensitivity and specificity sequence alignment software validation stem cells tetraodontiformes zebrafish

DIALIGNTool Content

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

Sequence Comparison > Multiple Sequence Alignments

Multiple alignment program which assembles a global sequence alignment from gap-free local pairwise alignments. This method could be especially useful when comparing large sequences that have only local similarities.

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tagsalgorithms amino acid sequence amino acid sequence homology animals chickens computational biology dna sequence analysis genome humans leukemia mice molecular sequence data neoplasm dna neoplasm genes nucleic acid regulatory sequences protein sequence analysis proteins rats sensitivity and specificity sequence alignment software validation stem cells tetraodontiformes zebrafish

IBM Bioinformatics and Pattern Discovery GroupTool Content

http://cbcsrv.watson.ibm.com/Tspd.html

DNA > Annotations
DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
RNA > Motifs
Sequence Comparison > Multiple Sequence Alignments

Extensive server possessing a wide range of tools for pattern discovery in DNA and protein sequences as well as in text. Tools for multiple sequence alignment, gene discovery, protein annotation, and other applications also exist on this server. A detailed help page is provided for all tools.

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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals anti-infective agents archaeal genes archaeal genome automated pattern recognition bacterial genes bacterial genome base sequence biomedical engineering chemical dictionaries computational biology conserved sequence dna dna sequence analysis eukaryotic cells evaluation studies as topic factual databases gene expression genetic databases genome genomics histones humans initiator codon leghemoglobin molecular models molecular sequence data open reading frames peptides probability protein databases protein sequence analysis proteins proteome rna sequence analysis secondary protein structure sequence alignment sequence analysis ubiquitin viral genome

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

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

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)

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 > Other Alignment Tools

E2GTool Content

http://bibiserv.techfak.uni-bielefeld.de/e2g/

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

E2G is a tool that maps a large set of EST and cDNA sequences to a user-supplied genomic sequence. The use of pre-computed indexed data structures increases the efficiency of the sequence comparison process, allowing a large amount of data to be mapped within a reasonable timeframe.

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tagsbase sequence chromosome mapping complementary dna expressed sequence tags genomics sequence alignment

Genotyping - NCBITool Content

http://www.ncbi.nih.gov/projects/genotyping/formpage.cgi

Model Organisms > Other Organisms
Sequence Comparison > Other Alignment Tools

The Genotyping tool at the NCBI identifies the genotype (or subtype) of viral sequences by using a sliding window approach to BLAST analysis against reference sequences for different viral subtypes. Results are shown as a graphical output plotting the top-scoring genotype. An alignment tool is also available.

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tagsalgorithms dna sequence analysis genetic recombination genotype hepacivirus hepatitis b virus hiv-1 molecular sequence data sequence alignment viral dna viral genes viral genome viruses
setsNational Center for Biotechnology Information (NCBI)

IMGT/V-QUESTTool Content

http://imgt.cines.fr/

Sequence Comparison > Other Alignment Tools

The international ImMunoGeneTics information system (IMGT) V-QUEry and STandardization (V-QUEST) tool compares a user-provided fasta-formatted germline or rearranged T cell receptor or immunoglobulin variable sequence with a reference set of sequences.

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tagsalgorithms animals b-lymphocyte gene rearrangement dna sequence analysis humans immunoglobulin fragments immunoglobulin genes immunoglobulin joining region immunoglobulin variable region mice rats sequence alignment systems integration t-lymphocyte gene rearrangement

IccareTool Content

http://genopole.toulouse.inra.fr/bioinfo/Iccare/

Sequence Comparison > Other Alignment Tools

The Iccare (Interspecific Comparative Clustering and Annotation foR Est) web server compares all available EST and mRNA sequences for a query organism against the set of transcripts for a reference organism. The results are presented graphically and relative to the location of genes on the chromosomes of the reference organism.

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tagsanimals arabidopsis chromosome mapping dna primers dna sequence analysis expressed sequence tags human genome humans messenger rna nucleic acid databases nucleic acid probes nucleic acid sequence homology plant genes rna sequence analysis rna splice sites systems integration

T-COFFEETool Content

http://www.tcoffee.org/

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

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

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

Sequence Comparison > Similarity Searching

BLASTTool Content

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

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

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

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

CHOPTool Content

http://www.rostlab.org/services/CHOP/

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

CHOP takes a protein sequence as input, and returns a list of protein sequence fragments with homology to PDB and Pfam domains and to proteins from the SWISS-PROT database.

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tagsalgorithms amino acid sequence homology protein sequence analysis proteomics tertiary protein structure

Meta-BASICTool Content

http://basic.bioinfo.pl/

Protein > 2-D Structure Prediction
Sequence Comparison > Similarity Searching

Meta-BASIC is a tool for detecting distant homologues using meta-profiles which combine both sequence positional variability and secondary structure.

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tagsalgorithms amino acid sequence homology glycosyltransferases molecular models protein sequence analysis protein structural homology proteins secondary protein structure sequence alignment trna methyltransferases

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

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

The European Bioinformatics Institute (EBI)Database Content

http://www.ebi.ac.uk

DNA > Databases
DNA > Sequence Retrieval and Submission
Education > Community
Education > Directories and Portals
Expression > Databases
Expression > Transcript Expression Analysis
Human Genome > Databases
Literature > Databases
Model Organisms > Databases
Other Molecules > Databases
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Databases
Protein > Domains and Motifs
Protein > Sequence Retrieval
RNA > Databases
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

The European Bioinformatics Institute (EMBL-EBI) provides access to a comprehensive, integrated set of biological data. Resources include information on genes, genomes, proteins, expression, literature, and molecular interactions as well as many other useful resources.

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tagsalgorithms animals biology computational biology europe gene expression profiling genetic databases humans nucleic acid databases nucleic acids phylogeny protein databases proteins sequence analysis sequence homology
setsEuropean Bioinformatics Institute (EBI)