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NAR Web Server Issue 2003

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Computer Related

DNA

Education

Expression

Human Genome

Literature

Model Organisms

Protein

RNA

Sequence Comparison

Computer Related > Math and Statistics

EVATool Content

http://cubic.bioc.columbia.edu/eva/

Computer Related > Math and Statistics
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.

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tagsautomation protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins reproducibility of results secondary protein structure sequence alignment

Computer Related > Web Services

XML Central of DDBJTool Content

http://www.xml.nig.ac.jp/index.html

Computer Related > Web Services
Education > Directories and Portals

XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.

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tagsbiology nucleic acid databases systems integration

DNA > Annotations

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

DNannotatorTool Content

http://bioapp.psych.uic.edu/DNannotator.htm

DNA > Annotations
Human Genome > Annotations

DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).

This content is being maintained by cliu.

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tagsalgorithms dna primers dna sequence analysis gene frequency genetic databases genetic markers genomics human chromosomes human genome humans sequence alignment sequence tagged sites single nucleotide polymorphism

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

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

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

DNA > DNA and Genomic Analysis

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

DNA > Gene Prediction

AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

DNA > Gene Prediction
Model Organisms > Microbes

Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

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tagsbacterial dna bacterial genes dna sequence analysis markov chains open reading frames

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

FrameDTool Content

http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD

DNA > Gene Prediction

FrameD is a program that predicts coding regions in prokaryotic and eukaryotic sequences that may contain frameshifts.

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tagsamino acid sequence homology bacterial genome complementary dna dna sequence analysis eukaryotic cells expressed sequence tags frameshift mutation gc rich sequence genes open reading frames

GeneFizzTool Content

http://pbga.pasteur.fr/GeneFizz/

DNA > Gene Prediction

GeneFizz is a tool for identifying genes using by using the physical characteristics of helix-to-coil transitions in DNA.

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tagsalgorithms animals biophysical phenomena biophysics computational biology dna dna sequence analysis drosophila melanogaster genes genetic code genetic models genetic techniques genomics molecular evolution nucleic acid conformation plasmodium falciparum protozoan dna protozoan genes protozoan genome

GeneSeqerTool Content

http://www.plantgdb.org/search/misc/PublicPlantSeq.php

DNA > Gene Prediction
Expression > Splicing
Model Organisms > Plants

GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.

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tagsarabidopsis complementary dna computational biology dna sequence analysis expressed sequence tags gene components genetic databases genetic transcription genomics nucleic acid repetitive sequences plant dna plant genes plant genome plant proteins plants protein sequence analysis sequence alignment

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

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

TRACTSTool Content

http://bioportal.weizmann.ac.il/tracts/tracts.html

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection

TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.

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tagsbase composition base sequence dna dna sequence analysis humans p53 genes purines pyrimidines

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

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

DNA > Phylogeny Reconstruction

NEWTDatabase Content

http://www.ebi.ac.uk/newt/display

DNA > Phylogeny Reconstruction
Model Organisms > General Resources
Protein > Phylogeny Reconstruction

NEWT is the taxonomy database maintained by the UniProt group.

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tagsclassification protein databases 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

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

PARSESNPTool Content

http://www.proweb.org/parsesnp/

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.

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tagsbase sequence dna sequence analysis mutation protein biosynthesis protein sequence analysis proteins sequence alignment single nucleotide polymorphism

SIFTTool Content

http://blocks.fhcrc.org/sift/SIFT.html

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function

Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.

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tagsamino acid motifs amino acid sequence amino acid substitution bacterial proteins bacteriophage t4 chromosome mapping computational biology conserved sequence dna sequence analysis escherichia coli proteins false positive reactions genes genetic polymorphism hiv protease hiv-1 humans inborn genetic diseases lac repressors lactose missense mutation molecular sequence data muramidase mutation phenotype probability protein databases protein sequence analysis proteins pseudogenes repressor proteins sequence alignment single nucleotide polymorphism

DNA > Sequence Retrieval and Submission

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

DNA > Structure and Sequence Feature Detection

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

Cluster BusterTool Content

http://zlab.bu.edu/cluster-buster/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.

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tagsbinding sites cluster analysis dna sequence analysis genetic code humans nucleic acid regulatory sequences transcription factors

Gibbs Motif SamplerTool Content

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

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

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

This content is being maintained by bbth.

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

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

INCLUSiveTool Content

http://www.esat.kuleuven.ac.be/inclusive

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

INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

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tagsalgorithms cluster analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis registries sequence analysis systems integration

MatchTool Content

http://www.gene-regulation.com/pub/programs.html#match

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.

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tagsalgorithms binding sites dna sequence analysis nucleic acid regulatory sequences 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

PromHTool Content

http://www.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promot...

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.

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tagsanimals conserved sequence dna sequence analysis genetic promoter regions genomics humans mice nucleic acid regulatory sequences transcription initiation site

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

REDUCETool Content

http://bussemaker.bio.columbia.edu/reduce/

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

REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.

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tagsalgorithms animals binding sites database management systems dna sequence analysis drosophila melanogaster gene expression profiling genetic transcription messenger rna nucleic acid regulatory sequences oligonucleotide array sequence analysis regression analysis saccharomyces cerevisiae software design transcription factors

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

SPattTool Content

http://stat.genopole.cnrs.fr/spatt/index.html

DNA > Structure and Sequence Feature Detection

Statistics for Patterns (SPatt) can compute the significance of a given DNA pattern in a genome sequence. This tool can be used to find patterns with unusual behaviour in DNA sequences.

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tagsalgorithms computer simulation dna sequence analysis markov chains nucleic acid regulatory sequences sequence alignment sequence analysis statistical data interpretation statistical models

SSATool Content

http://www.isrec.isb-sib.ch/ssa/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).

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tagsbacterial genome consensus sequence dna sequence analysis genetic promoter regions nucleic acid regulatory sequences protein biosynthesis response elements ribosomal rna transcription initiation site

SiteSeerTool Content

http://rocky.bms.umist.ac.uk/SiteSeer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.

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tags5' flanking region base sequence binding sites color dna sequence analysis fungal genes genetic promoter regions nucleic acid databases saccharomyces cerevisiae transcription factors

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

TRACTSTool Content

http://bioportal.weizmann.ac.il/tracts/tracts.html

DNA > Gene Prediction
DNA > Structure and Sequence Feature Detection

TRACTS calculates the frequencies, locations and lengths of all binary tracts (pairs of nucleotide combinations) in DNA sequences. Annotated output will include exon/intron regions and tract information.

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tagsbase composition base sequence dna dna sequence analysis humans p53 genes purines pyrimidines

Target ExplorerTool Content

http://luna.bioc.columbia.edu/Target_Explorer/

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

Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.

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tagsanimals binding sites dna sequence analysis drosophila melanogaster gene expression regulation genome humans nucleic acid regulatory sequences transcription factors

WEB-THERMODYNTool Content

http://www.gsa.buffalo.edu/dna/dk/WEBTHERMODYN/

DNA > Structure and Sequence Feature Detection

WEB-THERMODYN analyzes DNA sequences and computes the DNA helical stability. This tool can be used to predict sites of low helical stability present at regulatory regions for transcription and replication.

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tagsdeoxyribonucleases dna dna replication dna sequence analysis fungal chromosomes fungal dna mutation nucleic acid conformation nucleic acid denaturation nucleic acid regulatory sequences plasmids replication origin replicon saccharomyces cerevisiae thermodynamics

YMF 3.0Tool Content

http://wingless.cs.washington.edu/YMF/YMFWeb/YMFInput.pl

DNA > Structure and Sequence Feature Detection

YMF 3.0 (Yeast Motif Finder) is a tool that identifies good candidates for transcription factor binding sites by searching for statistically overrepresented motifs. Multiple organisms are supported including human, yeast, worm, plants, and microbes.

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tagsalgorithms binding sites dna sequence analysis genetic promoter regions mycobacterium tuberculosis nucleic acid regulatory sequences saccharomyces cerevisiae statistical data interpretation transcription factors

mrepsTool Content

http://bioinfo.lifl.fr/mreps/

DNA > Structure and Sequence Feature Detection

mreps is a tool for identifing tandemn repeats in DNA sequences.

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tagsalgorithms bacterial dna bacterial genes dna dna sequence analysis genetic polymorphism genomics human genome humans neisseria meningitidis saccharomyces cerevisiae tandem repeat sequences

rMotifTool Content

http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/

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

rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).

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tagsdna sequence analysis genetic promoter regions genetic transcription messenger rna nucleic acid regulatory sequences response elements

DNA > Tools For the Bench

CODEHOPTool Content

http://blocks.fhcrc.org/codehop.html

DNA > Tools For the Bench

COnsensus-DEgenerate Hybrid Oligonucleotide Primers (CODEHOP); degenerate PCR primer design; will accept unaligned sequences.

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tagsamino acid sequence base sequence consensus sequence dna primers oligonucleotides polymerase chain reaction protein sequence analysis sequence alignment

DePIETool Content

http://biocore.unl.edu/primer/primerPI.html

DNA > Tools For the Bench
Protein > Interactions, Pathways, Enzymes

Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.

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tagsdna primers nucleic acid databases nucleic acid denaturation polymerase chain reaction protein databases protein sorting signals proteins sequence analysis tertiary protein structure two-hybrid system techniques yeasts

NEBcutterTool Content

http://tools.neb.com/NEBcutter/index.php3

DNA > Tools For the Bench

NEBcutter finds non-overlapping open reading frames and sites for all enzymes that cut the sequence just once; max length is 100 kb.

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tagsdna methylation dna restriction enzymes dna sequence analysis plasmids restriction mapping substrate specificity type ii site-specific deoxyribonucleases

OligoWizTool Content

http://www.cbs.dtu.dk/services/OligoWiz2/

DNA > Tools For the Bench
Expression > Transcript Expression Analysis

OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.

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tagsalgorithms dna primers gene expression profiling genetic transcription molecular sequence data nucleic acid conformation nucleic acid denaturation oligonucleotide array sequence analysis oligonucleotide probes reproducibility of results rna sequence analysis saccharomyces cerevisiae systems integration temperature

PARSESNPTool Content

http://www.proweb.org/parsesnp/

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.

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tagsbase sequence dna sequence analysis mutation protein biosynthesis protein sequence analysis proteins sequence alignment single nucleotide polymorphism

PDATool Content

http://dbb.nhri.org.tw/primer/

DNA > Tools For the Bench

Primer Design Assistant (PDA) is a PCR primer design tool that will accept batch submissions of query sequences.

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tagsdimerization dna primers dna sequence analysis gc rich sequence nucleic acid conformation nucleic acid denaturation polymerase chain reaction thermodynamics

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)

ExPASy Molecular Biology ServerResource Content

http://www.expasy.org/

Education > Directories and Portals
Protein > Do-it-all Tools for Protein

Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.

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tagsenzymes gel electrophoresis molecular models protein conformation protein databases protein sequence analysis proteins proteomics systems integration

PBILTool Content

http://pbil.univ-lyon1.fr/

Education > Directories and Portals

Pole Bio-Informatique Lyonnais (PBIL) provides access to sequence databanks (EMBL, GenBank, SWISS-PROT, PIR) and to many tools of nucleic acid and protein sequence analyses.

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tagsdna sequence analysis genetic databases molecular models nucleic acids protein conformation protein sequence analysis proteins rna sequence analysis secondary protein structure sequence alignment sequence homology systems integration

Swiss EMBnetTool Content

http://www.ch.embnet.org/

Education > Directories and Portals

Swiss EMBnet is a web portal with links and access to various bioinformatics tools and links to institutes that are involved in bioinformatics.

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tagseurope protein databases protein sequence analysis sequence alignment

XML Central of DDBJTool Content

http://www.xml.nig.ac.jp/index.html

Computer Related > Web Services
Education > Directories and Portals

XML Central of the DNA Data Bank of Japan (DDBJ) provides SOAP (Simple Object Access Protocol) server and web services for various databases and bioinformatics programs.

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tagsbiology nucleic acid databases systems integration

Expression > Gene Regulation

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

Cluster BusterTool Content

http://zlab.bu.edu/cluster-buster/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Cluster Buster is a tool that finds clusters of pre-specified motifs in DNA sequences.

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tagsbinding sites cluster analysis dna sequence analysis genetic code humans nucleic acid regulatory sequences transcription factors

Gibbs Motif SamplerTool Content

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

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

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

This content is being maintained by bbth.

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

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

INCLUSiveTool Content

http://www.esat.kuleuven.ac.be/inclusive

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

INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

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tagsalgorithms cluster analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis registries sequence analysis systems integration

MatchTool Content

http://www.gene-regulation.com/pub/programs.html#match

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Match is a weight matrix-based tool which searches for putative transcription factor binding sites (TFBS) in DNA sequences. Registration at the site is free and is required to use Match.

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tagsalgorithms binding sites dna sequence analysis nucleic acid regulatory sequences 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

PromHTool Content

http://www.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promot...

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.

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tagsanimals conserved sequence dna sequence analysis genetic promoter regions genomics humans mice nucleic acid regulatory sequences transcription initiation site

REDUCETool Content

http://bussemaker.bio.columbia.edu/reduce/

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

REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.

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tagsalgorithms animals binding sites database management systems dna sequence analysis drosophila melanogaster gene expression profiling genetic transcription messenger rna nucleic acid regulatory sequences oligonucleotide array sequence analysis regression analysis saccharomyces cerevisiae software design transcription factors

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

SSATool Content

http://www.isrec.isb-sib.ch/ssa/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).

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tagsbacterial genome consensus sequence dna sequence analysis genetic promoter regions nucleic acid regulatory sequences protein biosynthesis response elements ribosomal rna transcription initiation site

SiteSeerTool Content

http://rocky.bms.umist.ac.uk/SiteSeer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SiteSeer is a visualization tool for mapping transcription factor binding sites (TFBS) in the upstream regions of single or grouped eukaryotic genes.

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tags5' flanking region base sequence binding sites color dna sequence analysis fungal genes genetic promoter regions nucleic acid databases saccharomyces cerevisiae transcription factors

Target ExplorerTool Content

http://luna.bioc.columbia.edu/Target_Explorer/

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

Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.

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tagsanimals binding sites dna sequence analysis drosophila melanogaster gene expression regulation genome humans nucleic acid regulatory sequences transcription factors

rMotifTool Content

http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/

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

rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).

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tagsdna sequence analysis genetic promoter regions genetic transcription messenger rna nucleic acid regulatory sequences response elements

Expression > Protein Expression

JVirGelTool Content

http://www.jvirgel.de/

Expression > Protein Expression
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics

JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.

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tagscomputer simulation gel electrophoresis isoelectric point molecular weight proteins proteomics reproducibility of results

Expression > Splicing

ESEfinderTool Content

http://rulai.cshl.edu/tools/ESE/

Expression > Splicing

ESEfinder is a web-based resource for identifing putative ESEs (exonic splicing enhancers), cis-acting motifs responsible for enhancing splicing.

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tagsbase sequence consensus sequence exons genetic enhancer elements humans messenger rna point mutation rna precursors rna sequence analysis rna splicing rna-binding proteins

GeneSeqerTool Content

http://www.plantgdb.org/search/misc/PublicPlantSeq.php

DNA > Gene Prediction
Expression > Splicing
Model Organisms > Plants

GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.

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tagsarabidopsis complementary dna computational biology dna sequence analysis expressed sequence tags gene components genetic databases genetic transcription genomics nucleic acid repetitive sequences plant dna plant genes plant genome plant proteins plants protein sequence analysis sequence alignment

Expression > Transcript Expression Analysis

ChipInfoTool Content

http://genomics.bioen.illinois.edu/chipinfo/

Expression > Transcript Expression Analysis

ChipInfo extracts gene annotation and gene ontology information from databases like NetAffx and Gene Ontology (GO) for microarray analysis. Output is provided in tabular format and the program is available for download for use on your own machine.

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tagsdna probes gene expression profiling genetic databases oligonucleotide array sequence analysis systems integration

ExpressYourselfTool Content

http://array.mbb.yale.edu/analysis/

Expression > Transcript Expression Analysis

ExpressYourself is a web-based platform to process microarray data. It includes tools for background correction, normalization, data processing and filtering.

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tagsalgorithms chromatin gene expression profiling genomics oligonucleotide array sequence analysis precipitin tests

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

GenePublisherTool Content

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

Expression > Transcript Expression Analysis

GenePublisher performs automatic normalization, statistical analysis, and visualization of DNA microarray data.

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tagsautomation cluster analysis gene expression profiling genetic databases genetic promoter regions metabolism nucleic acid regulatory sequences oligonucleotide array sequence analysis signal transduction

INCLUSiveTool Content

http://www.esat.kuleuven.ac.be/inclusive

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

INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.

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tagsalgorithms cluster analysis gene expression profiling nucleic acid regulatory sequences oligonucleotide array sequence analysis registries sequence analysis systems integration

OligoWizTool Content

http://www.cbs.dtu.dk/services/OligoWiz2/

DNA > Tools For the Bench
Expression > Transcript Expression Analysis

OligoWiz 2.0 is a client for microarray probe design that allows for the integration of sequence annotations, probe quality parameters, and the placement of multiple probes per transcript.

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tagsalgorithms dna primers gene expression profiling genetic transcription molecular sequence data nucleic acid conformation nucleic acid denaturation oligonucleotide array sequence analysis oligonucleotide probes reproducibility of results rna sequence analysis saccharomyces cerevisiae systems integration temperature

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

REDUCETool Content

http://bussemaker.bio.columbia.edu/reduce/

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

REDUCE uses a motif-based regression method for the identification of TFBS (transcription factor binding sites) from microarray data in yeast, worm and fly. A free registration is required.

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tagsalgorithms animals binding sites database management systems dna sequence analysis drosophila melanogaster gene expression profiling genetic transcription messenger rna nucleic acid regulatory sequences oligonucleotide array sequence analysis regression analysis saccharomyces cerevisiae software design transcription factors

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

Expression > cDNA, EST, SAGE

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

Human Genome > Annotations

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

DNannotatorTool Content

http://bioapp.psych.uic.edu/DNannotator.htm

DNA > Annotations
Human Genome > Annotations

DNannotator is a tool that performs de novo annotation of SNPs, STSs, and exons. It also allows for the migration of user-defined annotations onto different versions of genomic sequences (<30Kb size limit).

This content is being maintained by cliu.

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tagsalgorithms dna primers dna sequence analysis gene frequency genetic databases genetic markers genomics human chromosomes human genome humans sequence alignment sequence tagged sites single nucleotide polymorphism

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 > Sequence Polymorphisms

PARSESNPTool Content

http://www.proweb.org/parsesnp/

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.

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tagsbase sequence dna sequence analysis mutation protein biosynthesis protein sequence analysis proteins sequence alignment single nucleotide polymorphism

SIFTTool Content

http://blocks.fhcrc.org/sift/SIFT.html

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function

Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.

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tagsamino acid motifs amino acid sequence amino acid substitution bacterial proteins bacteriophage t4 chromosome mapping computational biology conserved sequence dna sequence analysis escherichia coli proteins false positive reactions genes genetic polymorphism hiv protease hiv-1 humans inborn genetic diseases lac repressors lactose missense mutation molecular sequence data muramidase mutation phenotype probability protein databases protein sequence analysis proteins pseudogenes repressor proteins sequence alignment single nucleotide polymorphism

Literature > Search Tools

XplorMedTool Content

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

Literature > Search Tools
Literature > Text Mining and Semantics

XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion.

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tagsalgorithms artificial intelligence benchmarking bibliography of medicine fuzzy logic genetic databases information systems medline publications systems integration

Literature > Text Mining and Semantics

XplorMedTool Content

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

Literature > Search Tools
Literature > Text Mining and Semantics

XplorMed is a tool that summarizes MEDLINE search results according to subjects and allows you to navigate through abstracts in an interactive fashion.

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tagsalgorithms artificial intelligence benchmarking bibliography of medicine fuzzy logic genetic databases information systems medline publications systems integration

Model Organisms > Fly

Target ExplorerTool Content

http://luna.bioc.columbia.edu/Target_Explorer/

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

Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.

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tagsanimals binding sites dna sequence analysis drosophila melanogaster gene expression regulation genome humans nucleic acid regulatory sequences transcription factors

Model Organisms > General Resources

NEWTDatabase Content

http://www.ebi.ac.uk/newt/display

DNA > Phylogeny Reconstruction
Model Organisms > General Resources
Protein > Phylogeny Reconstruction

NEWT is the taxonomy database maintained by the UniProt group.

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tagsclassification protein databases systems integration

Model Organisms > Microbes

AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html

Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast

Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

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tagsbacteria cell line fungi microbiological techniques reproducibility of results systems integration yeasts

AMIGeneTool Content

http://www.genoscope.cns.fr/agc/tools/amigene/Form/form.php

DNA > Gene Prediction
Model Organisms > Microbes

Annotation of MIcrobial Genes (AMIGene) is gene prediction server that can identify coding sequences in microbes.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genes dna sequence analysis markov chains open reading frames

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

JVirGelTool Content

http://www.jvirgel.de/

Expression > Protein Expression
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics

JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.

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tagscomputer simulation gel electrophoresis isoelectric point molecular weight proteins proteomics 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

Model Organisms > Other Organisms

AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html

Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast

Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

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tagsbacteria cell line fungi microbiological techniques reproducibility of results systems integration yeasts

Geno2phenoTool Content

http://www.geno2pheno.org/cgi-bin/geno2pheno.pl

Model Organisms > Other Organisms

Geno2pheno takes as input an HIV-1 pol-gene DNA sequence and estimates phenotypic drug resistance to 17 antiretroviral drugs.

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tagsalgorithms anti-hiv agents artificial intelligence automated pattern recognition cluster analysis computational biology computer-assisted drug therapy computing methodologies decision trees disease susceptibility dna sequence analysis drug combinations factual databases gene expression profiling genetic models genetic polymorphism genetic variation genotype hiv hiv infections hiv-1 humans innate immunity molecular sequence data phenotype pol genes regression analysis reproducibility of results sensitivity and specificity statistical models viral dna viral drug resistance viral genome

Model Organisms > Plants

EUGENE'HOMTool Content

http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl

DNA > Annotations
DNA > Gene Prediction
Model Organisms > Plants

EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. The data is currently tuned for plant sequences of up to 400kb.

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tagsalgorithms complementary dna dna sequence analysis eukaryotic cells genes genome initiator codon nucleic acid sequence homology plant dna rna splice sites

GeneSeqerTool Content

http://www.plantgdb.org/search/misc/PublicPlantSeq.php

DNA > Gene Prediction
Expression > Splicing
Model Organisms > Plants

GeneSeqer is a method to identify exon/intron structure by splice site prediction and spliced alignment in plant genomes.

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tagsarabidopsis complementary dna computational biology dna sequence analysis expressed sequence tags gene components genetic databases genetic transcription genomics nucleic acid repetitive sequences plant dna plant genes plant genome plant proteins plants protein sequence analysis sequence alignment

Model Organisms > Yeast

AHMIITool Content

http://www.wdcm.org/AHMII/ahmii.html

Model Organisms > Microbes
Model Organisms > Other Organisms
Model Organisms > Yeast

Agent to Help Microbial Information Integration (AHMII) offers a search engine for particular strains present in culture collections and databases in bacteria, fungi, yeasts and cell lines.

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tagsbacteria cell line fungi microbiological techniques reproducibility of results systems integration yeasts

rMotifTool Content

http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/

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

rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).

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tagsdna sequence analysis genetic promoter regions genetic transcription messenger rna nucleic acid regulatory sequences response elements

Protein > 2-D Structure Prediction

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

DSSPcontTool Content

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

Protein > 2-D Structure Prediction

DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.

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tagsalgorithms amino acid sequence biomolecular nuclear magnetic resonance hydrogen bonding molecular models proteins secondary protein structure

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

EVATool Content

http://cubic.bioc.columbia.edu/eva/

Computer Related > Math and Statistics
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.

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tagsautomation protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins reproducibility of results secondary protein structure sequence alignment

GlobPlotTool Content

http://globplot.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Domains and Motifs

GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.

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tagsalgorithms amino acid motifs humans molecular models protein sequence analysis proteome 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

NORSpTool Content

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

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

NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.

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tagsamino acids computational biology conserved sequence genetic transcription hydrogen bonding molecular evolution molecular models pliability protein binding protein databases protein folding protein sequence analysis proteins proteome secondary protein structure software design solvents structure-activity relationship

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

ProtinfoTool Content

http://protinfo.compbio.washington.edu/

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

Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.

This content is being maintained by lhhung.

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tagsalgorithms molecular models protein folding protein sequence analysis protein structural homology proteins secondary protein structure tertiary protein structure time factors

RbDeTool Content

http://icb.med.cornell.edu/crt/RbDe/index.xml

Protein > 2-D Structure Prediction
Protein > Presentation and Format

Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.

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tagsalgorithms amino acid sequence calmodulin connexins eye proteins factual databases humans membrane proteins membrane transport proteins molecular models molecular sequence data mutagenesis protein conformation protein folding proteins secondary protein structure src homology domains

SSEPTool Content

http://cluster.physics.iisc.ernet.in/ssep/options.html

Protein > 2-D Structure Prediction

Secondary Structural Elements of Proteins (SSEP) provides access to information about secondary structural elements present in non-redundant sets of proteins from the PDB.

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tagsartificial intelligence computational biology molecular models protein databases proteins secondary protein structure temperature x-ray crystallography

TMH BenchmarkTool Content

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

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

The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.

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tagsalgorithms animals computational biology hydrophobic and hydrophilic interactions membrane proteins molecular models protein folding protein sequence analysis reproducibility of results secondary protein structure sensitivity and specificity

VADARTool Content

http://redpoll.pharmacy.ualberta.ca/vadar/

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

Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.

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tagsalgorithms hydrogen bonding molecular structure protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure

Protein > 3-D Structural Features

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

CASTpTool Content

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

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

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

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

GlobPlotTool Content

http://globplot.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Domains and Motifs

GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.

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tagsalgorithms amino acid motifs humans molecular models protein sequence analysis proteome tertiary protein structure

MolSurferTool Content

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

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

Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

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tagsamino acid sequence animals dna hydrophobic and hydrophilic interactions ligands macromolecular substances molecular models molecular sequence data protein conformation protein databases proteins rna static electricity

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

PINTSTool Content

http://www.russell.embl.de/pints/

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

Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.

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tagsalgorithms animals binding sites factual databases humans molecular conformation molecular models protein conformation protein databases protein folding protein structural homology proteins quaternary protein structure sequence alignment sequence analysis tertiary protein structure

POPSTool Content

http://mathbio.nimr.mrc.ac.uk/wiki/POPS

Protein > 3-D Structural Features

Parameter OPtimised Surfaces (POPS) is an algorithm to calculate accessible surfaces areas at atomic and residue level.

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tagsalgorithms amino acids hydrophobic and hydrophilic interactions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein binding protein conformation proteins ribosomal proteins ribosomal rna ribosomes solvents time factors transfer rna

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

WebFEATURETool Content

http://feature.stanford.edu/webfeature/

Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

Protein > 3-D Structure Comparison

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

MATRASTool Content

http://strcomp.protein.osaka-u.ac.jp/matras/

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

MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.

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tagsalgorithms factual databases markov chains molecular evolution molecular models protein databases protein folding protein structural homology proteins secondary protein structure sequence alignment

PINTSTool Content

http://www.russell.embl.de/pints/

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

Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.

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tagsalgorithms animals binding sites factual databases humans molecular conformation molecular models protein conformation protein databases protein folding protein structural homology proteins quaternary protein structure sequence alignment sequence analysis tertiary protein structure

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

T-COFFEETool Content

http://www.tcoffee.org/

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

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

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

Protein > 3-D Structure Prediction

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

EVATool Content

http://cubic.bioc.columbia.edu/eva/

Computer Related > Math and Statistics
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction

EValuation of Automatic protein structure prediction; provides a continuous, automated, statistical analysis of structure prediction servers.

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tagsautomation protein conformation protein databases protein folding protein sequence analysis protein structural homology proteins reproducibility of results secondary protein structure sequence alignment

ModellerTool Content

http://salilab.org/modeller/

Protein > 3-D Structure Prediction

Homology or comparative modeling of 3D protein structures.

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins biological models carrier proteins computer simulation enzymes factual databases genetic models genome genomics humans kallikreins l-lactate dehydrogenase mathematics molecular models molecular sequence data pancreatic elastase probability protein conformation protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure theoretical models thermodynamics tissue kallikreins trichomonas vaginalis trypsin

NORSpTool Content

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

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

NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.

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tagsamino acids computational biology conserved sequence genetic transcription hydrogen bonding molecular evolution molecular models pliability protein binding protein databases protein folding protein sequence analysis proteins proteome secondary protein structure software design solvents structure-activity relationship

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

ProtinfoTool Content

http://protinfo.compbio.washington.edu/

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

Protinfo takes a protein sequence as input and returns the atomic coordinates for a prediction of tertiary structure for that protein. Predictions can be made by comparative or de novo modelling.

This content is being maintained by lhhung.

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tagsalgorithms molecular models protein folding protein sequence analysis protein structural homology proteins secondary protein structure tertiary protein structure time factors

Swiss ModelTool Content

http://www.expasy.ch/swissmod/SWISS-MODEL.html

Protein > 3-D Structure Prediction

Automated protein modelling server.

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tagsalgorithms amino acid sequence amino acid sequence homology animals artificial intelligence automation chemical models computational biology computer simulation factual databases genome humans molecular models molecular sequence data online systems protein conformation protein databases protein sequence analysis protein structural homology proteins reproducibility of results sequence alignment switzerland systems integration

VADARTool Content

http://redpoll.pharmacy.ualberta.ca/vadar/

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

Volume, Area, Dihedral Angle Reporter (VADAR) is a web server for qualitative evaluation of protein structure data.

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tagsalgorithms hydrogen bonding molecular structure protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure

Protein > 3-D Structure Retrieval/Viewing

3MatrixTool Content

http://motif.stanford.edu/distributions/3matrix/

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

3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.

This content is being maintained by brutlag.

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tagsamino acid motifs amino acids animals conserved sequence molecular models protein conformation protein databases proteins sequence alignment

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/

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

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.

This content is being maintained by brutlag.

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tagsamino acid motifs amino acid sequence amino acids animals conserved sequence database management systems molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment three-dimensional imaging

CASTpTool Content

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

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

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

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

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

Motif3DTool Content

http://umber.sbs.man.ac.uk/dbbrowser/motif3d/motif3d.html

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

Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.

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tagsamino acid motifs animals molecular models protein conformation protein databases proteins rhodopsin

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

SEMTool Content

http://dicsoft2.physics.iisc.ernet.in/sem/

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

Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary.

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tagsmolecular models nucleic acids proteins

Protein > Annotation and Function

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

NAR Web Server Issue 2005NAR Web Server Issue 2003
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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

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

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

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

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

SIFTTool Content

http://blocks.fhcrc.org/sift/SIFT.html

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms
Protein > Annotation and Function

Sorting Intolerant From Tolerant (SIFT) is a sequence homology-based tool that will predict whether an amino acid substitution will affect protein function.

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tagsamino acid motifs amino acid sequence amino acid substitution bacterial proteins bacteriophage t4 chromosome mapping computational biology conserved sequence dna sequence analysis escherichia coli proteins false positive reactions genes genetic polymorphism hiv protease hiv-1 humans inborn genetic diseases lac repressors lactose missense mutation molecular sequence data muramidase mutation phenotype probability protein databases protein sequence analysis proteins pseudogenes repressor proteins sequence alignment single nucleotide polymorphism

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

Protein > Biochemical Features

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

MolSurferTool Content

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

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

Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

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tagsamino acid sequence animals dna hydrophobic and hydrophilic interactions ligands macromolecular substances molecular models molecular sequence data protein conformation protein databases proteins rna static electricity

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

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

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

The Mendel SiteTool Content

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

Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.

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tagsacyltransferases amino acid motifs animals eukaryotic cells fungal proteins glycine glycosylphosphatidylinositols lipid metabolism molecular sequence data myristic acids peroxisomes plant proteins post-translational protein processing protein sequence analysis protein sorting signals proteins protozoan proteins viral proteins

Protein > Databases

ELMTool Content

http://elm.eu.org/

Protein > Databases
Protein > Domains and Motifs

Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

NAR Database Issue 2010NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology eukaryotic cells genetic databases humans molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins tertiary protein structure

Protein > Do-it-all Tools for Protein

ExPASy Molecular Biology ServerResource Content

http://www.expasy.org/

Education > Directories and Portals
Protein > Do-it-all Tools for Protein

Expert Protein Analysis System; programs and databases for the analysis of protein sequences, structures and 2-D PAGE.

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tagsenzymes gel electrophoresis molecular models protein conformation protein databases protein sequence analysis proteins proteomics systems integration

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

Protein > Domains and Motifs

3MatrixTool Content

http://motif.stanford.edu/distributions/3matrix/

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

3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.

This content is being maintained by brutlag.

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tagsamino acid motifs amino acids animals conserved sequence molecular models protein conformation protein databases proteins sequence alignment

3MotifTool Content

http://motif.stanford.edu/distributions/3motif/

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

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.

This content is being maintained by brutlag.

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tagsamino acid motifs amino acid sequence amino acids animals conserved sequence database management systems molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment three-dimensional imaging

CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/

Protein > Domains and Motifs
Protein > Sequence Features

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.

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tagsamino acid sequence biochemistry dna sequence analysis humans molecular sequence data neoplasm proteins neural networks (computer) phosphoproteins phosphorylation phosphoserine phosphothreonine phosphotyrosine protein sequence analysis proteins radioactive tracers recombinant proteins sensitivity and specificity

ELMTool Content

http://elm.eu.org/

Protein > Databases
Protein > Domains and Motifs

Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

NAR Database Issue 2010NAR Web Server Issue 2003
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tagsamino acid motifs amino acid sequence amino acid sequence homology animals computational biology eukaryotic cells genetic databases humans molecular sequence data nucleic acid databases protein databases protein sequence analysis proteins tertiary protein structure

Gibbs Motif SamplerTool Content

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

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

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

This content is being maintained by bbth.

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

GlobPlotTool Content

http://globplot.embl.de/

Protein > 2-D Structure Prediction
Protein > 3-D Structural Features
Protein > Domains and Motifs

GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.

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tagsalgorithms amino acid motifs humans molecular models protein sequence analysis proteome 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.

NAR Web Server Issue 2003NAR Web Server Issue 2004
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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

Motif3DTool Content

http://umber.sbs.man.ac.uk/dbbrowser/motif3d/motif3d.html

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

Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.

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tagsamino acid motifs animals molecular models protein conformation protein databases proteins rhodopsin

PARSESNPTool Content

http://www.proweb.org/parsesnp/

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.

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tagsbase sequence dna sequence analysis mutation protein biosynthesis protein sequence analysis proteins sequence alignment single nucleotide polymorphism

PINTSTool Content

http://www.russell.embl.de/pints/

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

Patterns in Non-homologous Tertiary Structures (PINTS) finds similarities between protein structures containing structural patterns and provides a statistical measure of local structural similiarities.

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tagsalgorithms animals binding sites factual databases humans molecular conformation molecular models protein conformation protein databases protein folding protein structural homology proteins quaternary protein structure sequence alignment sequence analysis tertiary protein structure

PipeAlignTool Content

http://bips.u-strasbg.fr/PipeAlign/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial proteins caenorhabditis elegans cluster analysis computational biology conserved sequence cytoplasmic and nuclear receptors factual databases fungal proteins gene expression profiling genetic transcription genomics haemophilus influenzae humans leukemia molecular sequence data phylogeny predictive value of tests protein databases protein sequence analysis proteins pyrococcus reproducibility of results saccharomyces cerevisiae sensitivity and specificity sequence alignment small nuclear ribonucleoproteins

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

SEARCHPKSTool Content

http://www.nii.res.in/searchpks.html

Protein > Domains and Motifs

SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.

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tagsamino acid sequence homology molecular models multienzyme complexes protein sequence analysis substrate specificity tertiary protein structure

SIRWTool Content

http://sirw.embl.de/

Protein > Domains and Motifs
Protein > Sequence Retrieval

SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif.

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tagsamino acid motifs protein databases protein sequence analysis

SVM-PROTTool Content

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

Protein > Domains and Motifs
Protein > Sequence Features

Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.

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tagsamino acid sequence amino acid sequence homology protein sequence analysis proteins

ScansiteTool Content

http://scansite.mit.edu/

Protein > Domains and Motifs

Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.

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tagsalgorithms amino acid motifs amino acid sequence animals binding sites cattle cdc2 protein kinase cdc2-cdc28 kinases computational biology consensus sequence cyclic amp-dependent protein kinases cyclin-dependent kinase 2 cyclin-dependent kinases factual databases fungal proteins genome humans mice mitogen-activated protein kinase kinases molecular models molecular sequence data molecular structure peptides phosphorylation protein binding protein conformation protein databases protein interaction mapping protein kinases protein sequence analysis protein-serine-threonine kinases proteins proteome rats saccharomyces cerevisiae proteins serine signal transduction substrate specificity tertiary protein structure threonine tyrosine

The Mendel SiteTool Content

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

Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.

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tagsacyltransferases amino acid motifs animals eukaryotic cells fungal proteins glycine glycosylphosphatidylinositols lipid metabolism molecular sequence data myristic acids peroxisomes plant proteins post-translational protein processing protein sequence analysis protein sorting signals proteins protozoan proteins viral proteins

WebFEATURETool Content

http://feature.stanford.edu/webfeature/

Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

iSPOTTool Content

http://cbm.bio.uniroma2.it/ispot/

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

iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.

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tagsalgorithms amino acid sequence animals binding sites computational biology factual databases humans ligands molecular models molecular sequence data multigene family peptide fragments peptide library probability protein binding protein databases protein sequence analysis proteins sequence alignment src homology domains substrate specificity tertiary protein structure

Protein > Interactions, Pathways, Enzymes

DePIETool Content

http://biocore.unl.edu/primer/primerPI.html

DNA > Tools For the Bench
Protein > Interactions, Pathways, Enzymes

Design Primers for Protein Interaction Experiments (DePIE) is a web-based primer design tool for protein interaction experiments.

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tagsdna primers nucleic acid databases nucleic acid denaturation polymerase chain reaction protein databases protein sorting signals proteins sequence analysis tertiary protein structure two-hybrid system techniques yeasts

MolSurferTool Content

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

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

Molsurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. It can be used to study protein-protein and protein-DNA/RNA interfaces.

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tagsamino acid sequence animals dna hydrophobic and hydrophilic interactions ligands macromolecular substances molecular models molecular sequence data protein conformation protein databases proteins rna static electricity

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

iSPOTTool Content

http://cbm.bio.uniroma2.it/ispot/

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

iSPOT (Sequence Prediction Of Target) uses experimental interaction data combined with structural residue-residue contact information to predict the peptide binding specificity of SH3, PDZ, and WW domains.

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tagsalgorithms amino acid sequence animals binding sites computational biology factual databases humans ligands molecular models molecular sequence data multigene family peptide fragments peptide library probability protein binding protein databases protein sequence analysis proteins sequence alignment src homology domains substrate specificity tertiary protein structure

Protein > Localization and Targeting

Loc3DDatabase Content

http://cubic.bioc.columbia.edu/db/LOC3d/

Protein > Localization and Targeting

LOC3D is a database of predicted subcellular localization for eukaryotic proteins of known three-dimensional (3D) structure and includes tools to predict the subcellular localization for submitted protein sequences.

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tagsalgorithms amino acid sequence homology amino acids animals chloroplasts computational biology computer simulation eukaryotic cells humans neural networks (computer) nuclear localization signals plant proteins protein conformation protein databases protein sequence analysis protein transport proteins proteome reproducibility of results secondary protein structure sequence alignment subcellular fractions

PSORT.orgTool Content

http://www.psort.org/

Protein > Localization and Targeting

PSORT.org provides links to the PSORT family of web-based programs for subcellular localization prediction, including PSORTb and WoLF PSORT, well as other datasets and resources relevant to localization prediction.

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tagsalgorithms amino acid sequence bacterial outer membrane proteins bacterial proteins bayes theorem binding sites cell membrane computational biology cytoplasm decision trees escherichia coli evaluation studies as topic expert systems factual databases fungal proteins gram-negative bacteria humans lipoproteins membrane proteins molecular sequence data neural networks (computer) protein databases protein precursors protein sequence analysis protein sorting signals proteins reproducibility of results saccharomyces cerevisiae secondary protein structure sequence alignment subcellular fractions

TMH BenchmarkTool Content

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

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

The Transmembrane Helix (TMH) Benchmark server provides a standard benchmark evaluation for helical trans-membrane prediction methods.

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tagsalgorithms animals computational biology hydrophobic and hydrophilic interactions membrane proteins molecular models protein folding protein sequence analysis reproducibility of results secondary protein structure sensitivity and specificity

The Mendel SiteTool Content

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

Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting

The Mendel Site contains a collection of tools for predicting lipid postranslational modifications and localization signals in protein sequences.

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tagsacyltransferases amino acid motifs animals eukaryotic cells fungal proteins glycine glycosylphosphatidylinositols lipid metabolism molecular sequence data myristic acids peroxisomes plant proteins post-translational protein processing protein sequence analysis protein sorting signals proteins protozoan proteins viral proteins

Protein > Molecular Dynamics and Docking

Andrej Sali LabResource Content

http://salilab.org/our_resources.shtml

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

This page contains various resources for comparative protein structure modelling and analysis from the Sali Lab at University of California at San Francisco (UCSF).

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tagsamino acid sequence amino acid sequence homology animals bacterial proteins carrier proteins l-lactate dehydrogenase molecular models molecular sequence data protein databases protein folding protein structural homology proteins reproducibility of results sequence alignment sequence homology systems integration tertiary protein structure trichomonas vaginalis

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

Protein > Phylogeny Reconstruction

NEWTDatabase Content

http://www.ebi.ac.uk/newt/display

DNA > Phylogeny Reconstruction
Model Organisms > General Resources
Protein > Phylogeny Reconstruction

NEWT is the taxonomy database maintained by the UniProt group.

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tagsclassification protein databases systems integration

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

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

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

RbDeTool Content

http://icb.med.cornell.edu/crt/RbDe/index.xml

Protein > 2-D Structure Prediction
Protein > Presentation and Format

Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.

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tagsalgorithms amino acid sequence calmodulin connexins eye proteins factual databases humans membrane proteins membrane transport proteins molecular models molecular sequence data mutagenesis protein conformation protein folding proteins secondary protein structure src homology domains

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 > Protein Expression

JVirGelTool Content

http://www.jvirgel.de/

Expression > Protein Expression
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics

JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.

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tagscomputer simulation gel electrophoresis isoelectric point molecular weight proteins proteomics reproducibility of results

Protein > Proteomics

JVirGelTool Content

http://www.jvirgel.de/

Expression > Protein Expression
Model Organisms > Microbes
Protein > Protein Expression
Protein > Proteomics

JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.

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tagscomputer simulation gel electrophoresis isoelectric point molecular weight proteins proteomics reproducibility of results

Protein > Sequence Comparison

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

STING MilleniumTool Content

http://luna.bioc.columbia.edu/SMS/STINGm/

Protein > 3-D Structural Features
Protein > 3-D Structure Comparison
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Phylogeny Reconstruction
Protein > Sequence Comparison

STING is a suite of tools for the analysis of protein sequence, structure, stability and function - and the relationships between them.

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tagsacid anhydride hydrolases algorithms alpha-amylases amino acid sequence amino acid sequence homology amino acids animals beetles binding sites chemical models chymotrypsin color computational biology computer simulation conserved sequence enzyme inhibitors fabaceae hiv integrase hydrogen bonding lectins medicinal plants molecular cloning molecular models molecular sequence data molecular structure online systems ovomucin plant lectins plant proteins proprotein convertases protein binding protein conformation protein databases protein interaction mapping protein sequence analysis protein structural homology proteins quaternary protein structure recombinant proteins sequence alignment structure-activity relationship systems integration x-ray crystallography

Protein > Sequence Features

CRPDatabase Content

http://fasta.bioch.virginia.edu/crp/

Protein > Domains and Motifs
Protein > Sequence Features

Cleaved Radioactivity of Phosphopeptides (CRP) performs in silico proteolytic cleavage of protein sequences and reports the radioactivity that would be observed if a given serine, threonine or tyrosine were phosphorylated.

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tagsamino acid sequence biochemistry dna sequence analysis humans molecular sequence data neoplasm proteins neural networks (computer) phosphoproteins phosphorylation phosphoserine phosphothreonine phosphotyrosine protein sequence analysis proteins radioactive tracers recombinant proteins sensitivity and specificity

NRSASTool Content

http://www.receptors.org/NR/servers/html/

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Do-it-all Tools for Protein
Protein > Molecular Dynamics and Docking
Protein > Sequence Features

Nuclear Receptor Structure Analysis Server (NRSAS) is a multi-purpose collection of tools for the analyses of nuclear hormone receptors.

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tagscytoplasmic and nuclear receptors hormones hydrogen bonding molecular models mutation protein conformation protein structural homology

SVM-PROTTool Content

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

Protein > Domains and Motifs
Protein > Sequence Features

Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.

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tagsamino acid sequence amino acid sequence homology protein sequence analysis proteins

Protein > Sequence Retrieval

BLAST2SRSTool Content

http://blast2srs.embl.de/

Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.

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tagsamino acid sequence homology animals humans protein databases

BioverseTool Content

http://bioverse.compbio.washington.edu/

DNA > Annotations
Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Prediction
Protein > Annotation and Function
Protein > Sequence Comparison
Protein > Sequence Retrieval

Bioverse is a system that uses computational techniques to facilitate exploring the relationships between molecular, genomic, proteomic, systems and organismal information.

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tagsamino acid sequence homology biological models chromosome mapping computer simulation energy metabolism gene expression profiling gene expression regulation molecular models protein conformation protein interaction mapping protein sequence analysis proteins proteome proteomics signal transduction

SIRWTool Content

http://sirw.embl.de/

Protein > Domains and Motifs
Protein > Sequence Retrieval

SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search protein/nucleotide databases with keywords and a sequence motif.

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tagsamino acid motifs protein databases protein sequence analysis

UniqueProtTool Content

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

Protein > Sequence Retrieval

UniqueProt creates representative protein sequence sets by eliminating sequence redundancy based on sequence similiarity. This tool needs to be downloaded and run locally on your own machine.

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tagsalgorithms protein sequence analysis proteins sequence alignment tertiary protein structure

RNA > General Resources

RNA StudioTool Content

http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_RNA_Studio.html

RNA > General Resources
RNA > Structure Prediction, Visualization, and Design

RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization.

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tagsbase sequence computational biology nucleic acid conformation rna

RNA > Motifs

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

NDB ToolsTool Content

http://ndbserver.rutgers.edu/services/

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

The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.

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tagsalgorithms base pairing base sequence chemical models dna factual databases molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology proteins restriction mapping ribosomal rna rna signal recognition particle statistical data interpretation stereoisomerism terminology as topic water

RNA AnalyzerTool Content

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

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

RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.

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tagscatalytic rna messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

WebFEATURETool Content

http://feature.stanford.edu/webfeature/

Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

RNA > Sequence Retrieval

RSATTool Content

http://rsat.ccb.sickkids.ca/

DNA > DNA and Genomic Analysis
DNA > Sequence Retrieval and Submission
DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
RNA > Motifs
RNA > Sequence Retrieval

Regulatory Sequence Analysis Tools (RSAT) detects regulatory signals in non-coding sequences; tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Tools may be accessed separately or connected to other tools. As well, the tools are available as web services for integration into programmatic work flows. New tools incorporated include an automated sequence retrieval from EnsEMBL, motif comparison and motif quality tools, and the capacity to process ChIP-sequence data.

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tags5' flanking region algorithms binding sites computational biology dna sequence analysis dna-binding proteins fungal gene expression regulation fungal genes fungal genome genetic transcription genome genomics nucleic acid regulatory sequences oligodeoxyribonucleotides saccharomyces cerevisiae transcription factors transcriptional regulatory elements yeasts

RNA > Structure Prediction, Visualization, and Design

MfoldTool Content

http://mfold.rna.albany.edu/?q=mfold/download-mfold

RNA > Structure Prediction, Visualization, and Design

Predict RNA secondary structure from sequence; does not predict pseudoknots - see PKNOTS.

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tagsbase composition base sequence consensus sequence dna molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid denaturation nucleic acid hybridization nucleic acid repetitive sequences rna single-stranded dna thermodynamics

NDB ToolsTool Content

http://ndbserver.rutgers.edu/services/

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

The Nucleic Acid Database (NDB) Tools page includes RNAView and BPView, programs for the visualization and classification of RNA base pairs, motifs, and structures.

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tagsalgorithms base pairing base sequence chemical models dna factual databases molecular models molecular sequence data nucleic acid conformation nucleic acid databases nucleic acid sequence homology proteins restriction mapping ribosomal rna rna signal recognition particle statistical data interpretation stereoisomerism terminology as topic water

PSEUDOVIEWERTool Content

http://pseudoviewer.inha.ac.kr/

RNA > Structure Prediction, Visualization, and Design

PSEUDOVIEWER is a tool for visualizing RNA pseudoknot structures.

This content is being maintained by khan.

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tagsalgorithms base pairing base sequence computational biology molecular models molecular sequence data nucleic acid conformation programming languages rna rna sequence analysis

PfoldTool Content

http://www.daimi.au.dk/~compbio/pfold

RNA > Structure Prediction, Visualization, and Design

The Pfold server takes an alignment of RNA sequences as input and predicts a common secondary structure.

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tagsalgorithms bacterial rna base sequence biological evolution catalytic rna computational biology computer simulation endoribonucleases molecular evolution molecular models molecular sequence data nucleic acid conformation nucleic acid sequence homology probability reproducibility of results ribonuclease p rna rna sequence analysis sequence alignment stochastic processes time factors

RNA AnalyzerTool Content

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

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

RNA Analyzer searches for known structures and identifies RNA motifs in your input sequence.

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tagscatalytic rna messenger rna nucleic acid conformation ribonucleic acid regulatory sequences rna sequence analysis

RNA StudioTool Content

http://bibiserv.techfak.uni-bielefeld.de/bibi/Tools_RNA_Studio.html

RNA > General Resources
RNA > Structure Prediction, Visualization, and Design

RNA Studio contains software for RNA analyses including tools for structure prediction, comparison, and visualization.

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tagsbase sequence computational biology nucleic acid conformation rna

RNAsoftTool Content

http://www.rnasoft.ca/

RNA > Structure Prediction, Visualization, and Design

Software for RNA/DNA secondary structure prediction and design

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tagsalgorithms base sequence computer simulation dna genetic databases genetic models molecular sequence data nucleic acid conformation rna

SEMTool Content

http://dicsoft2.physics.iisc.ernet.in/sem/

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

Symmetry Equivalent Molecules (SEM) is a tool for generating symmetrically equivalent three-dimensional (3D) molecules. This web based tool incorporates the graphics package of RASMOL for visualization; some configuration necessary.

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tagsmolecular models nucleic acids proteins

Vienna RNA PackageTool Content

http://www.tbi.univie.ac.at/~ivo/RNA/

RNA > Structure Prediction, Visualization, and Design

Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.

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tagsalgorithms nucleic acid conformation rna rna sequence analysis sequence alignment

WebFEATURETool Content

http://feature.stanford.edu/webfeature/

Protein > 3-D Structural Features
Protein > Domains and Motifs
RNA > Motifs
RNA > Structure Prediction, Visualization, and Design

WebFEATURE is a structural analysis tool for identifying 3D physiochemical motifs in molecular structures.

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tagsalgorithms bayes theorem binding sites calcium calcium-binding proteins computational biology factual databases genomics likelihood functions macromolecular substances molecular models molecular structure nucleic acid conformation nucleic acids protein conformation proteins reproducibility of results sensitivity and specificity statistical models

Sequence Comparison > Alignment Editing and Visualization

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

ESPriptTool Content

http://espript.ibcp.fr/ESPript/ESPript/index.php

Sequence Comparison > Alignment Editing and Visualization

Easy Sequencing in Postscript (ESPript) is a utility which provides postscript output for aligned sequences with graphical enhancements and structural information.

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tagsamino acid sequence amino acid sequence homology dna-binding proteins molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

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

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

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

Sequence Comparison > Analysis of Aligned Sequences

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure 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

PARSESNPTool Content

http://www.proweb.org/parsesnp/

DNA > Sequence Polymorphisms
DNA > Tools For the Bench
Human Genome > Sequence Polymorphisms
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences

Project Aligned Related Sequences and Evaluate SNPs (PARSESNP) is a tool for the analysis of polymorphisms in genes.

NAR Web Server Issue 2003
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tagsbase sequence dna sequence analysis mutation protein biosynthesis protein sequence analysis proteins sequence alignment single nucleotide polymorphism

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

PipMakerTool Content

http://bio.cse.psu.edu/

Sequence Comparison > Analysis of Aligned Sequences

PipMaker computes alignments of similar regions in two DNA sequences. MultiPipMaker allows the user to see relationships among more than two sequences.

NAR Web Server Issue 2003
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tagsalgorithms animals bacterial genes base sequence binding sites caenorhabditis elegans cats computational biology dna dna sequence analysis escherichia coli genomics helminth genes horses humans mice molecular sequence data nucleic acid regulatory sequences phylogeny proto-oncogene proteins protozoan genes salmonella typhimurium sequence alignment transcription factors wnt2 protein

PipeAlignTool Content

http://bips.u-strasbg.fr/PipeAlign/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial proteins caenorhabditis elegans cluster analysis computational biology conserved sequence cytoplasmic and nuclear receptors factual databases fungal proteins gene expression profiling genetic transcription genomics haemophilus influenzae humans leukemia molecular sequence data phylogeny predictive value of tests protein databases protein sequence analysis proteins pyrococcus reproducibility of results saccharomyces cerevisiae sensitivity and specificity sequence alignment small nuclear ribonucleoproteins

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 > Comparative Genomics

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella 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

TIGR Software ToolsResource Content

http://www.tigr.org/software/

DNA > Annotations
DNA > Gene Prediction
DNA > Mapping and Assembly
DNA > Structure and Sequence Feature Detection
Expression > Transcript Expression Analysis
Sequence Comparison > Comparative Genomics

A list of open-source software packages available for free from The Institute for Genomic Research (TIGR).

NAR Web Server Issue 2003
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tagsarabidopsis dna sequence analysis eukaryotic cells exons genes introns markov chains plant genes

Sequence Comparison > Multiple Sequence Alignments

ALGGENTool Content

http://alggen.lsi.upc.es/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ALLGEN server provides various tools for multiple sequence alignments, clustering, and assembly of ESTs. It also includes search tools for transcription factor binding sites (TFBS), repeated patterns, and transposons.

NAR Web Server Issue 2003
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tagsalgorithms animals binding sites chickens chromosome mapping computational biology conserved sequence dna dna sequence analysis gene expression profiling genetic promoter regions genome genomics humans mice nucleic acid conformation nucleic acid databases nucleic acid regulatory sequences nucleic acid repetitive sequences nucleic acid sequence homology rats sequence alignment software design species specificity transcription factors x-ray crystallography

ClustalWTool Content

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

Sequence Comparison > Multiple Sequence Alignments

Standard multiple sequence alignment.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence globins molecular sequence data nucleic acids phylogeny protein sequence analysis proteins secondary protein structure sensitivity and specificity sequence alignment sequence analysis

ENDscriptTool Content

http://espript.ibcp.fr/ESPript/ENDscript/index.php

Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

ENDscript is a tool for creating, visualizing, and interpreting multiple sequence alignments overlayed with known structural information.

NAR Web Server Issue 2003
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tagsamino acid sequence amino acid sequence homology data display database management systems dna-binding proteins factual databases molecular models molecular sequence data molecular structure protein conformation protein databases protein sequence analysis proteins secondary protein structure sequence alignment tertiary protein structure transcription factors

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

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

MATRASTool Content

http://strcomp.protein.osaka-u.ac.jp/matras/

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

MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.

NAR Web Server Issue 2003
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tagsalgorithms factual databases markov chains molecular evolution molecular models protein databases protein folding protein structural homology proteins secondary protein structure sequence alignment

PipeAlignTool Content

http://bips.u-strasbg.fr/PipeAlign/

Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments

PipeAlign takes one or more protein sequences as input and analyzes them in a five-step process during which searches for sequence homologues, analyses of multiple sequence alignments, and hierarchical relationships between protein subfamilies are performed.

NAR Web Server Issue 2003
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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial proteins caenorhabditis elegans cluster analysis computational biology conserved sequence cytoplasmic and nuclear receptors factual databases fungal proteins gene expression profiling genetic transcription genomics haemophilus influenzae humans leukemia molecular sequence data phylogeny predictive value of tests protein databases protein sequence analysis proteins pyrococcus reproducibility of results saccharomyces cerevisiae sensitivity and specificity sequence alignment small nuclear ribonucleoproteins

RevTransTool Content

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

Sequence Comparison > Multiple Sequence Alignments

RevTrans takes a set of DNA sequences, virtually translates them, aligns the peptide sequences, and uses this as a scaffold for constructing the corresponding DNA multiple alignment.

NAR Web Server Issue 2003
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tagsamino acid substitution base sequence codon dna sequence analysis mutation protein sequence analysis sequence alignment

T-COFFEETool Content

http://www.tcoffee.org/

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

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

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

Sequence Comparison > Other Alignment Tools

T-COFFEETool Content

http://www.tcoffee.org/

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

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

NAR Web Server Issue 2003NAR Web Server Issue 2004NAR Web Server Issue 2006NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid motifs amino acid sequence amino acid sequence homology animals base sequence computational biology computer simulation consensus sequence dna dna sequence analysis evaluation studies as topic factual databases fibronectins genes genetic models humans messenger rna molecular sequence data phylogeny protein conformation protein databases protein sequence analysis protein-serine-threonine kinases proteins reproducibility of results rna sequence analysis sensitivity and specificity sequence alignment

Sequence Comparison > Pairwise Sequence Alignments

EnteriXTool Content

http://enterix.cbcb.umd.edu/

Model Organisms > Microbes
Sequence Comparison > Alignment Editing and Visualization
Sequence Comparison > Comparative Genomics
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

EnteriX is a collection of tools for viewing pairwise and multiple alignments for bacterial genome sequences.

NAR Web Server Issue 2003
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tagsbacterial dna bacterial genome conserved sequence dna sequence analysis enterobacteriaceae escherichia coli gene components gene deletion genomics nucleic acid regulatory sequences nucleotidyltransferases salmonella sequence alignment

MATRASTool Content

http://strcomp.protein.osaka-u.ac.jp/matras/

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

MATRAS is a resource for comparing protein three dimensional (3D) structures. Users can compare protein 3D structures using pairwise alignments, multiple alignments, or by a comparing against a library of known structures.

NAR Web Server Issue 2003
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tagsalgorithms factual databases markov chains molecular evolution molecular models protein databases protein folding protein structural homology proteins secondary protein structure sequence alignment

Sequence Comparison > Similarity Searching

BLAST2SRSTool Content

http://blast2srs.embl.de/

Protein > Sequence Retrieval
Sequence Comparison > Similarity Searching

BLAST2SRS (Sequence Retrieval System) is a tool to retrieve protein sequences using similarity (BLAST) and keyword searches.

NAR Web Server Issue 2003
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tagsamino acid sequence homology animals humans protein databases

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