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NAR Web Server Issue 2005

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Computer Related

DNA

Education

Expression

Human Genome

Literature

Model Organisms

Other Molecules

Protein

RNA

Sequence Comparison

Computer Related > Bio-* Programming Tools

CCTTool Content

http://sourceforge.net/projects/orb-cct

Computer Related > Bio-* Programming Tools

CCT (Current Comparative Table) is a software package that you can install and set-up on your own system to help you to maintain and search databases.

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tagscomputational biology genomics nucleic acid databases protein databases

Computer Related > Math and Statistics

EVAconTool Content

http://www.pdg.cnb.uam.es/eva/con/index.html

Computer Related > Math and Statistics
Protein > 3-D Structural Features

EVAcon automates the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.

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tagsamino acids molecular models protein conformation reproducibility of results

Computer Related > Web Services

EBI ToolsTool Content

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

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

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

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

DNA > Annotations

BASysTool Content

http://basys.ca

DNA > Annotations
Model Organisms > Microbes

BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.

This content is being maintained by gary.vandomselaar@gmail.com.

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tagsbacterial chromosomes bacterial genome genomics plasmids

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

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

FeatureExtractTool Content

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

DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

InterProScanTool Content

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

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

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.

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tagsdatabase management systems dna sequence analysis humans protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

MICheckTool Content

http://www.genoscope.cns.fr/agc/tools/micheck/

DNA > Annotations

MICheck (Microbial Genome Checker) allows the user to verify gene annotations in previously published microbial genomes.

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tagsbacterial genes bacterial genome genomics nucleic acid databases reproducibility of results time factors

MutDBDatabase Content

http://www.mutdb.org/

DNA > Annotations
DNA > Sequence Polymorphisms

MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.

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tagsamino acid substitution database management systems documentation genetic databases genetic predisposition to disease genetic variation human genome humans molecular models mutation phenotype protein conformation protein databases protein sequence analysis proteins sequence alignment single nucleotide polymorphism structure-activity relationship

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

WebGestaltTool Content

http://bioinfo.vanderbilt.edu/webgestalt/

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

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.

This content is being maintained by bzhang.

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tagsgene expression genes genetic databases genomics humans proteomics statistical data interpretation systems integration tissue distribution

DNA > Gene Prediction

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

GeneMarkTool Content

http://opal.biology.gatech.edu/GeneMark/

DNA > Gene Prediction

The GeneMark family of programs employ Markov models and are specifically tuned for gene prediction for sequences from prokaryotes, viral genomes and eukaryotes.

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tagsalgorithms animals bacterial genes computational biology genes genomics humans markov chains viral genes

DNA > Mapping and Assembly

Projector 2Tool Content

http://molgen.biol.rug.nl/websoftware/projector2/

DNA > Mapping and Assembly
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps.

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tagsalgorithms bacterial genome contig mapping dna primers genomics polymerase chain reaction

DNA > Phylogeny Reconstruction

MLSTTool Content

http://www.mlst.net/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

POWERTool Content

http://power.nhri.org.tw/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with aligned sequences.

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tagsalgorithms dna sequence analysis phylogeny protein sequence analysis rna sequence analysis sequence alignment systems integration

DNA > Sequence Polymorphisms

ARTSDatabase Content

http://andromeda.gsf.de/arts

DNA > Sequence Polymorphisms
Model Organisms > Mouse and Rat

ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.

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tagsanimals chromosome mapping genetic markers genomics genotype inbred c3h mice mice mutant strains mice single nucleotide polymorphism

AutoSNPdbTool Content

http://autosnpdb.qfab.org.au/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.

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tagsdna sequence analysis sequence alignment single nucleotide polymorphism time factors

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

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

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

ISTECH SNPAnalyzerTool Content

http://snp.istech.info/istech/board/login_form.jsp

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

ISTECH SNPAnalyzer is a tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required; some browser requirements and set-up necessary.

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tagsalgorithms dna sequence analysis gene frequency genetic predisposition to disease genotype haplotypes humans linkage disequilibrium phenotype quantitative trait loci single nucleotide polymorphism systems integration

MutDBDatabase Content

http://www.mutdb.org/

DNA > Annotations
DNA > Sequence Polymorphisms

MutDB is a database that associates protein structural information with mutations and polymorphisms in gene sequences. The data is derived from dbSNP and Swiss-Prot, and can be browsed by gene name or searched by keyword or by various identifiers.

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tagsamino acid substitution database management systems documentation genetic databases genetic predisposition to disease genetic variation human genome humans molecular models mutation phenotype protein conformation protein databases protein sequence analysis proteins sequence alignment single nucleotide polymorphism structure-activity relationship

SNP CutterTool Content

http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.

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tagsdna primers dna restriction enzymes genotype humans polymerase chain reaction restriction fragment length polymorphism single nucleotide polymorphism

nsSNPAnalyzerTool Content

http://snpanalyzer.uthsc.edu/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.

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tagsalgorithms artificial intelligence computational biology genetic predisposition to disease humans phenotype protein conformation protein sequence analysis sequence alignment single nucleotide polymorphism

DNA > Sequence Retrieval and Submission

EBI ToolsTool Content

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

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

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

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

FeatureExtractTool Content

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

DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

MRSTool Content

http://mrs.cmbi.ru.nl/

DNA > Sequence Retrieval and Submission
Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Retrieval

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.

This content is being maintained by maarten.

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tagsgenetic databases nucleic acid databases protein databases time factors

DNA > Structure and Sequence Feature Detection

ARGOTool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

CONREALTool Content

http://conreal.niob.knaw.nl/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

CisMolsTool Content

http://cismols.cchmc.org/

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

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

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tagsbase sequence binding sites conserved sequence gene expression regulation genomics response elements transcription factors

FooterTool Content

http://biodev.hgen.pitt.edu/Footer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

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tagsalgorithms animals binding sites dna footprinting dna sequence analysis gene expression regulation genetic promoter regions mammals phylogeny transcription factors

JCatTool Content

http://www.jcat.de/

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

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.

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tagsalgorithms animals caenorhabditis elegans codon escherichia coli gene expression pseudomonas aeruginosa recombinant proteins species specificity

Onto-ToolsTool Content

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

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

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

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

POCOTool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.

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tagsbinding sites computational biology down-regulation gene expression regulation genetic promoter regions genomics transcription factors up-regulation

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Protein > Domains and Motifs
RNA > Motifs

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

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tagsarabidopsis arabidopsis proteins dna sequence analysis peptides plant dna protein sequence analysis

PromoterPlotTool Content

http://promoterplot.fmi.ch/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used as input for a local installation of the tool.

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tagsalgorithms animals binding sites gene expression regulation genetic promoter regions genomics humans mice rats transcription factors

RibExTool Content

http://www.ibt.unam.mx/biocomputo/RibEx.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved

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tagsbacterial gene expression regulation bacterial rna base sequence conserved sequence dna sequence analysis open reading frames ribonucleic acid regulatory sequences

SynoRTool Content

http://synor.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SynoR searches vertebrate genomes for synonymous regulatory elements.

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tagsanimals binding sites cardiac myocytes gene expression regulation genomics humans mice rats response elements transcription factors vertebrates

T-Reg ComparatorTool Content

http://treg.molgen.mpg.de/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).

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tagsbinding sites gene expression regulation genomics nucleic acid regulatory sequences transcription factors

TOUCAN 2Tool Content

http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

TOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.

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tagsalgorithms binding sites cell cycle proteins computational biology dna sequence analysis dna-binding proteins e2f transcription factors gene expression regulation genetic promoter regions genomics human genome humans liver muscles nucleic acid regulatory sequences transcription factors

WordSpyTool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

WordSpy allows the user to search for over-represented words in a set of sequences and to search for discriminative words using negative sequence data. WordSpy employs this functionality as a means to search for transcription factor binding motifs.

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tagsalgorithms binding sites gene expression regulation genetic promoter regions genomics statistical models terminology as topic transcription factors

DNA > Tools For the Bench

ASePCRTool Content

http://genome.ewha.ac.kr/ASePCR/

DNA > Tools For the Bench
Expression > Splicing

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

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tagsalgorithms alternative splicing animals base sequence expressed sequence tags humans messenger rna mice molecular sequence data rats reverse transcriptase polymerase chain reaction tissue distribution

Assembly PCR Oligo MakerTool Content

http://publish.yorku.ca/~pjohnson/AssemblyPCRoligomaker.html

DNA > Tools For the Bench

Assembly PCR Oligo Maker is a tool for designing oligodeoxynucleotides for the PCR based construction of long DNA molecules.

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tagsdna oligodeoxyribonucleotides polymerase chain reaction rna synthetic genes

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt

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

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

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tagsalgorithms animals bacterial rna base sequence calorimetry dna dna sequence analysis fungal rna genetic hybridization introns molecular sequence data nucleic acid conformation nucleic acid denaturation nucleic acid hybridization oligonucleotides oligoribonucleotides phylogeny rats rna rna sequence analysis single-stranded dna structure-activity relationship temperature theoretical models transition temperature

E-RNAiTool Content

http://e-rnai.dkfz.de/

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

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

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

PriFiTool Content

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

DNA > Tools For the Bench
Sequence Comparison > Analysis of Aligned Sequences

PriFi is a tool for designing and evaluating primer pairs based on the input of a DNA sequence alignment; useful for the PCR amplification of homologs.

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tagsdna primers genomics nucleic acid sequence homology phylogeny polymerase chain reaction sequence alignment

Stitchprofiles.uio.noTool Content

http://stitchprofiles.uio.no/

DNA > Tools For the Bench

Stitchprofiles.uio.no is a server that performs web-based computations on DNA melting. In addition to creating stitch profile diagrams representing the alternative conformations that partly melted DNA can adopt, the server can also plot the classical melting curves, probability profiles, and temperature profiles.

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tagsalgorithms base sequence dna dna sequence analysis nucleic acid conformation nucleic acid denaturation statistical models temperature thermodynamics

dsCheckTool Content

http://dscheck.rnai.jp/

DNA > Tools For the Bench
Expression > Gene Regulation

dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs.

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tagsalgorithms animals double-stranded rna rna interference rna sequence analysis small interfering rna

Education > Directories and Portals

Bioinformatics Links DirectoryResource Content

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

Education > Directories and Portals

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

This content is being maintained by Francis Ouellette.

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

EBI ToolsTool Content

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

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

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

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

Expression > Gene Regulation

ARGOTool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.

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tagsalgorithms binding sites eukaryotic cells gene expression regulation genetic promoter regions genomics transcription factors

AntiHunter 2.0Tool Content

http://bio.ifom-ieo-campus.it/antihunter

Expression > Gene Regulation
Expression > cDNA, EST, SAGE

AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.

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tagsalgorithms antisense rna dna sequence analysis expressed sequence tags genetic databases sequence alignment time factors

AthaMapDatabase Content

http://www.athamap.de/

Expression > Gene Regulation
Model Organisms > Plants

AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

This content is being maintained by Reinhard Hehl.

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tagsarabidopsis arabidopsis proteins base sequence binding sites cold temperature computational biology conserved sequence dehydration genetic databases genetic transcription genomics molecular sequence data nucleic acid databases plant dna plant gene expression regulation plant genes plant genome protein binding response elements sequence alignment systems integration transcription factors transcriptional regulatory elements untranslated rna

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

CONREALTool Content

http://conreal.niob.knaw.nl/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

CONREAL (Conserved Regulatory Elements Anchored Alignment) allows identification of transcription factor binding sites (TFBS) that are conserved between two orthologous promoter sequences.

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tagsalgorithms animals base sequence binding sites conserved sequence dna footprinting dna sequence analysis dna-binding proteins gene expression regulation genetic promoter regions hepatocyte nuclear factor 3-beta humans mice nuclear proteins nucleic acid regulatory sequences nucleic acid sequence homology phylogeny rats sequence alignment takifugu transcription factors zebrafish

CisMolsTool Content

http://cismols.cchmc.org/

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

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

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tagsbase sequence binding sites conserved sequence gene expression regulation genomics response elements transcription factors

E-RNAiTool Content

http://e-rnai.dkfz.de/

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

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

FooterTool Content

http://biodev.hgen.pitt.edu/Footer/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.

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tagsalgorithms animals binding sites dna footprinting dna sequence analysis gene expression regulation genetic promoter regions mammals phylogeny transcription factors

MicroInspectorTool Content

http://bioinfo.uni-plovdiv.bg/microinspector/

Expression > Gene Regulation
RNA > Functional RNAs
RNA > Motifs

MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.

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tagsbase pairing binding sites messenger rna micrornas rna sequence analysis

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

POCOTool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.

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tagsbinding sites computational biology down-regulation gene expression regulation genetic promoter regions genomics transcription factors up-regulation

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Protein > Domains and Motifs
RNA > Motifs

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

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tagsarabidopsis arabidopsis proteins dna sequence analysis peptides plant dna protein sequence analysis

PromoterPlotTool Content

http://promoterplot.fmi.ch/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

PromoterPlot takes the output from a TransFac search as input, and finds similarities between groups of promoters in an attempt to simplify the results of transcription factor searches. FASTA/Affymetrix IDs can also be used as input for a local installation of the tool.

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tagsalgorithms animals binding sites gene expression regulation genetic promoter regions genomics humans mice rats transcription factors

RibExTool Content

http://www.ibt.unam.mx/biocomputo/RibEx.html

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

Riboswitch Explorer (RibEx) searches sequences for known riboswitches and also for predicted bacterial regulatory elements that are highly conserved

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tagsbacterial gene expression regulation bacterial rna base sequence conserved sequence dna sequence analysis open reading frames ribonucleic acid regulatory sequences

SynoRTool Content

http://synor.dcode.org/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

SynoR searches vertebrate genomes for synonymous regulatory elements.

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tagsanimals binding sites cardiac myocytes gene expression regulation genomics humans mice rats response elements transcription factors vertebrates

T-Reg ComparatorTool Content

http://treg.molgen.mpg.de/

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

T-Reg Comparator is a tool for the analysis of transcriptional regulation that allows you to compare a set of position weight matrices (PWM) against the T-Reg database (a collection of PWMs built from Transfac and Jaspar).

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tagsbinding sites gene expression regulation genomics nucleic acid regulatory sequences transcription factors

TOUCAN 2Tool Content

http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

TOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.

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tagsalgorithms binding sites cell cycle proteins computational biology dna sequence analysis dna-binding proteins e2f transcription factors gene expression regulation genetic promoter regions genomics human genome humans liver muscles nucleic acid regulatory sequences transcription factors

WordSpyTool Content

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

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation

WordSpy allows the user to search for over-represented words in a set of sequences and to search for discriminative words using negative sequence data. WordSpy employs this functionality as a means to search for transcription factor binding motifs.

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tagsalgorithms binding sites gene expression regulation genetic promoter regions genomics statistical models terminology as topic transcription factors

dsCheckTool Content

http://dscheck.rnai.jp/

DNA > Tools For the Bench
Expression > Gene Regulation

dsCheck takes a nucleotide sequence as input and estimates off-target effects caused by dsRNA (double-stranded RNA) employed in RNAi studies. dsCheck can be used either to verify previously designed dsRNA sequences, or to design off-target minimized dsRNAs.

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miRUTool Content

http://bioinfo.noble.org/gateway/index.php?option=com_content&task=view&id=53&It...

Expression > Gene Regulation
RNA > Functional RNAs

miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.

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Expression > Gene Set Analysis

VisANTTool Content

http://visant.bu.edu/

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

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

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

Expression > Networks

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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VisANTTool Content

http://visant.bu.edu/

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

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

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

Expression > Protein Expression

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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VisANTTool Content

http://visant.bu.edu/

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

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

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

Expression > Splicing

ASePCRTool Content

http://genome.ewha.ac.kr/ASePCR/

DNA > Tools For the Bench
Expression > Splicing

ASePCR (Alternative Splicing electronic PCR) is a tool for carrying out e-PCR to detect differences in amplicon sizes in transcripts from different tissues and organs.

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tagsalgorithms alternative splicing animals base sequence expressed sequence tags humans messenger rna mice molecular sequence data rats reverse transcriptase polymerase chain reaction tissue distribution

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

Expression > Transcript Expression Analysis

ArrayXPathTool Content

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

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

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

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

BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

Expression ProfilerTool Content

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

Expression > Transcript Expression Analysis

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

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tagsgene expression profiling genomics oligonucleotide array sequence analysis

GEMSTool Content

http://genomics10.bu.edu/terrence/gems/

Expression > Transcript Expression Analysis

GEMS (Gene Expression Mining Server) is a tool for biclustering microarray data. It is available as a web tool and as a standalone command-line program.

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tagsalgorithms cluster analysis gene expression profiling oligonucleotide array sequence analysis

GEPASTool Content

http://www.gepas.org

DNA > Sequence Polymorphisms
Expression > Transcript Expression Analysis

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

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

GFINDerTool Content

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

Expression > Transcript Expression Analysis

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

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

MIDAWTool Content

http://midaw.cribi.unipd.it/dnachip/

Expression > Transcript Expression Analysis

MIDAW (MIcroarray Data Analysis Web tool) is a data normalization and analysis tool for microarray data.

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tagsalgorithms gene expression profiling normal distribution oligonucleotide array sequence analysis statistical data interpretation

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

Pathway ExplorerTool Content

https://pathwayexplorer.genome.tugraz.at/

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

Pathway Explorer is a tool for visualizing high throughput expression data simultaneously with biological pathway data available from KEGG, BioCarta, and GenMAPP.

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tagsgene expression profiling genetic databases oligonucleotide array sequence analysis systems integration

RACETool Content

http://race.unil.ch/

Expression > Transcript Expression Analysis

RACE (Remote Analysis Computation for gene Expression data) is a collection of web tools designed to assist with the analysis of DNA microarray data and results.

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tagscomputational biology gene expression profiling oligonucleotide array sequence analysis

T-profilerTool Content

http://www.t-profiler.org/

Expression > Transcript Expression Analysis
Model Organisms > Yeast

T-profiler is a tool for the analysis of gene expression data from yeast that uses the t-test to score changes in the average activity of pre-defined groups of genes.

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tagsalgorithms candida albicans gene expression profiling oligonucleotide array sequence analysis saccharomyces cerevisiae

VisANTTool Content

http://visant.bu.edu/

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

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

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

WebGestaltTool Content

http://bioinfo.vanderbilt.edu/webgestalt/

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

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.

This content is being maintained by bzhang.

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tagsgene expression genes genetic databases genomics humans proteomics statistical data interpretation systems integration tissue distribution

Expression > cDNA, EST, SAGE

AntiHunter 2.0Tool Content

http://bio.ifom-ieo-campus.it/antihunter

Expression > Gene Regulation
Expression > cDNA, EST, SAGE

AnitHunter 2.0 is a tool to detect potential EST antisense transcripts within a given genomic region from the analysis of BLAST output.

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tagsalgorithms antisense rna dna sequence analysis expressed sequence tags genetic databases sequence alignment time factors

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Protein > Domains and Motifs
RNA > Motifs

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

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tagsarabidopsis arabidopsis proteins dna sequence analysis peptides plant dna protein sequence analysis

Human Genome > Annotations

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

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

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

FeatureExtractTool Content

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

DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

InterProScanTool Content

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

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

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.

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tagsdatabase management systems dna sequence analysis humans protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

Human Genome > Health and Disease

GeneSeekerTool Content

http://www.cmbi.ru.nl/GeneSeeker/

Human Genome > Health and Disease

GeneSeeker allows you to generate a list of candidate genes related to a human genetic disorder by searching against localization and expression databases.

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tagschromosome mapping gene expression genetic databases genetic predisposition to disease humans inborn genetic diseases phenotype syndrome systems integration

PEPVACTool Content

http://immunax.dfci.harvard.edu/PEPVAC/

Human Genome > Health and Disease
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

PEPVAC is a tool to assist in the development of multi-epitope vaccines. It is optimized for this task by predicting peptides with the ability to bind to several human leukocyte antigens that have similar peptide binding specificity.

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tagshla-a antigens hla-b antigens humans ligands peptides proteasome endopeptidase complex protein sequence analysis t-lymphocyte epitopes vaccines

Human Genome > Other Resources

DCODE.ORGResource Content

http://www.dcode.org/

Human Genome > Other Resources
Sequence Comparison > Comparative Genomics

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

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tagsbase sequence binding sites computational biology gene expression regulation genetic promoter regions genomics humans molecular evolution nucleic acid regulatory sequences phylogeny sequence alignment transcription factors

WikiGeneResource Content

http://andromeda.gsf.de/wiki

Human Genome > Other Resources

WikiGene is a scientific project that follows a community-based approach to collect data about genes and gene regulatory events.

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tagsgene expression regulation pubmed

Human Genome > Sequence Polymorphisms

AutoSNPdbTool Content

http://autosnpdb.qfab.org.au/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

SNPServer combines BLAST, cap3 and a SNP discovery module into a single pipeline for the discovery of SNPs in user submitted files or dynamically created assemblies.

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tagsdna sequence analysis sequence alignment single nucleotide polymorphism time factors

ISTECH SNPAnalyzerTool Content

http://snp.istech.info/istech/board/login_form.jsp

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

ISTECH SNPAnalyzer is a tool for the statistical analysis of SNP data that includes Hardy Weinberg equilibrium (HWE), haplotype estimation, linkage disequilibrium (LD), and QTL analyses. Registration required; some browser requirements and set-up necessary.

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tagsalgorithms dna sequence analysis gene frequency genetic predisposition to disease genotype haplotypes humans linkage disequilibrium phenotype quantitative trait loci single nucleotide polymorphism systems integration

SNP CutterTool Content

http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

SNP Cutter is a tool that automates PCR-RFLP assay design for SNP genotyping.

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tagsdna primers dna restriction enzymes genotype humans polymerase chain reaction restriction fragment length polymorphism single nucleotide polymorphism

nsSNPAnalyzerTool Content

http://snpanalyzer.uthsc.edu/

DNA > Sequence Polymorphisms
Human Genome > Sequence Polymorphisms

nsSNPAnalyzer is a tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) is phenotypically neutral or disease associated.

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tagsalgorithms artificial intelligence computational biology genetic predisposition to disease humans phenotype protein conformation protein sequence analysis sequence alignment single nucleotide polymorphism

Literature > Search Tools

EBI ToolsTool Content

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

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

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

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

GoPubMedTool Content

http://www.gopubmed.org/

Literature > Search Tools

GoPubMed is a tool that allows users to explore the results of PubMed queries in the context of Gene Ontology (GO) terms.

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tagscontrolled vocabulary enzyme inhibitors genetic databases levamisole pubmed subject headings

Literature > Text Mining and Semantics

LitMinerTool Content

http://andromeda.gsf.de/litminer

Literature > Text Mining and Semantics

LitMiner is a literature data mining tool that is based on the annotation of key terms in article abstracts followed by statistical co-citation analysis of annotated key terms in order to predict relationships between genes, compounds, diseases and phenotypes, and tissues and organs.

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tagsgene expression regulation pubmed

Model Organisms > Fly

E-RNAiTool Content

http://e-rnai.dkfz.de/

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

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

Model Organisms > General Resources

InterProScanTool Content

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

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

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.

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tagsdatabase management systems dna sequence analysis humans protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

JCatTool Content

http://www.jcat.de/

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

JCAT (Java Codon Adaptation Tool) is a tool that can adjust the codon usage of an input sequence to the selected organism. Useful for improving the expression of foreign genes in hosts with different codon usage.

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tagsalgorithms animals caenorhabditis elegans codon escherichia coli gene expression pseudomonas aeruginosa recombinant proteins species specificity

Model Organisms > Microbes

BASysTool Content

http://basys.ca

DNA > Annotations
Model Organisms > Microbes

BASys (Bacterial Annotation System) is a tool for automated annotation of bacterial genomic (chromosomal and plasmid) sequences including gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weights, isoelectric points, operon structures, subcellular localization, signal peptides, transmembrane regions, secondary structures, 3-D structures, reactions, and pathways.

This content is being maintained by gary.vandomselaar@gmail.com.

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tagsbacterial chromosomes bacterial genome genomics plasmids

BROPResource Content

http://brop.org/

Expression > Transcript Expression Analysis
Model Organisms > Microbes

The Bioinformatics Resource for Oral Pathogens (BROP) contains tools for genomics of oral pathogens including Genome Viewer, GOAL (genome wide ORF alignment), an oral pathogen microarray database, an entrez counter, oral pathogen specific BLAST, and a codon usage database.

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tagsbacteria bacterial capsules bacterial genes bacterial genome bacterial polysaccharides bacterial proteins biological evolution computational biology dna transposable elements fungal genome genetic databases genetic variation genomic islands genomics horizontal gene transfer integrases mouth oligonucleotide array sequence analysis open reading frames operon porphyromonas gingivalis sequence alignment streptococcus mutans transfer rna virulence virulence factors

MLSTTool Content

http://www.mlst.net/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

Projector 2Tool Content

http://molgen.biol.rug.nl/websoftware/projector2/

DNA > Mapping and Assembly
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps.

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tagsalgorithms bacterial genome contig mapping dna primers genomics polymerase chain reaction

Model Organisms > Mouse and Rat

ARTSDatabase Content

http://andromeda.gsf.de/arts

DNA > Sequence Polymorphisms
Model Organisms > Mouse and Rat

ARTS (Advanced Retrieval Tool for SNPs) can be used to retrieve SNP that are polymorphic between several different mouse strains to aid in the design of genome-wide SNP marker panels.

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tagsanimals chromosome mapping genetic markers genomics genotype inbred c3h mice mice mutant strains mice single nucleotide polymorphism

Model Organisms > Other Organisms

E-RNAiTool Content

http://e-rnai.dkfz.de/

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

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

Model Organisms > Plants

AthaMapDatabase Content

http://www.athamap.de/

Expression > Gene Regulation
Model Organisms > Plants

AthaMap is a genome-wide map of putative transcription factor binding sites in Arabidopsis thaliana

This content is being maintained by Reinhard Hehl.

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tagsarabidopsis arabidopsis proteins base sequence binding sites cold temperature computational biology conserved sequence dehydration genetic databases genetic transcription genomics molecular sequence data nucleic acid databases plant dna plant gene expression regulation plant genes plant genome protein binding response elements sequence alignment systems integration transcription factors transcriptional regulatory elements untranslated rna

Model Organisms > Yeast

E-RNAiTool Content

http://e-rnai.dkfz.de/

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

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

SCMDDatabase Content

http://scmd.gi.k.u-tokyo.ac.jp/

Model Organisms > Yeast

The Sacharomyces Cerevisiae Morphological Database (SCMD) is a collection of micrographs of budding yeast mutants; visualization and data mining tools are provided.

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tagscell cycle computational biology computer-assisted image processing factual databases fluorescence microscopy genetic databases mutation saccharomyces cerevisiae

T-profilerTool Content

http://www.t-profiler.org/

Expression > Transcript Expression Analysis
Model Organisms > Yeast

T-profiler is a tool for the analysis of gene expression data from yeast that uses the t-test to score changes in the average activity of pre-defined groups of genes.

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tagsalgorithms candida albicans gene expression profiling oligonucleotide array sequence analysis saccharomyces cerevisiae

Other Molecules > Carbohydrates

GlyprotTool Content

http://www.glycosciences.de/modeling/glyprot/php/main.php

Other Molecules > Carbohydrates
Protein > 3-D Structural Features

Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.

This content is being maintained by luetteke.

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tagscomputational biology glycoproteins glycosylation humans molecular models protein conformation protein isoforms

SEARCHGTrTool Content

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

Other Molecules > Carbohydrates
Protein > Domains and Motifs

SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs.

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tagsanti-bacterial agents binding sites computational biology glycosylation glycosyltransferases metabolism protein conformation protein sequence analysis substrate specificity

Protein > 2-D Structure Prediction

BhairPredTool Content

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

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

BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.

This content is being maintained by raghavagps.

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tagsalgorithms artificial intelligence neural networks (computer) protein sequence analysis secondary protein structure sequence alignment

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

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

PRALINETool Content

http://ibivu.cs.vu.nl/programs/pralinewww/

Protein > 2-D Structure Prediction
Sequence Comparison > Multiple Sequence Alignments

Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.

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tagsacid anhydride hydrolases algorithms amino acid motifs amino acid sequence amino acid sequence homology amino acids bacterial proteins binding sites cluster analysis computational biology consensus sequence cytochrome p-450 enzyme system database management systems discriminant analysis flavodoxin genetic databases hiv integrase membrane proteins molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment systems integration tertiary protein structure

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

SCRATCHTool Content

http://www.igb.uci.edu/servers/psss.html

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

SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.

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tagsdisulfides mutation protein conformation proteins secondary protein structure solvents tertiary protein structure

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

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

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

TMBETA-NETTool Content

http://psfs.cbrc.jp/tmbeta-net/

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

Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.

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tagsalgorithms amino acid sequence amino acids bacterial outer membrane proteins cell membrane factual databases membrane proteins molecular models neural networks (computer) reproducibility of results secondary protein structure

TRAMPLETool Content

http://gpcr.biocomp.unibo.it/biodec/

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

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial outer membrane proteins biological models chemical models computer security computer simulation database management systems double-blind method escherichia coli evaluation studies as topic factual databases forecasting haemophilus influenzae humans markov chains membrane proteins molecular models molecular sequence data neural networks (computer) porins protein folding protein sequence analysis protein sorting signals reproducibility of results rhodopseudomonas secondary protein structure sequence alignment software design statistical models

Protein > 3-D Structural Features

BhairPredTool Content

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

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

BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.

This content is being maintained by raghavagps.

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tagsalgorithms artificial intelligence neural networks (computer) protein sequence analysis secondary protein structure sequence alignment

CHC_FINDTool Content

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

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

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

ConSurfTool Content

http://consurf.tau.ac.il/

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

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

EVAconTool Content

http://www.pdg.cnb.uam.es/eva/con/index.html

Computer Related > Math and Statistics
Protein > 3-D Structural Features

EVAcon automates the continuous evaluation of inter-residue contact prediction servers. Results can be viewed statically or dynamically generated.

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tagsamino acids molecular models protein conformation reproducibility of results

FF - Fragment FinderTool Content

http://cluster.physics.iisc.ernet.in/ff/

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

FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.

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tagsamino acid motifs molecular structure proteins

GlyprotTool Content

http://www.glycosciences.de/modeling/glyprot/php/main.php

Other Molecules > Carbohydrates
Protein > 3-D Structural Features

Glyprot is a tool for predicting and modelling all potential N-glycosylation sites in a given 3D structure.

This content is being maintained by luetteke.

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tagscomputational biology glycoproteins glycosylation humans molecular models protein conformation protein isoforms

H++Tool Content

http://biophysics.cs.vt.edu/H++

Protein > 3-D Structural Features
Protein > Biochemical Features

H++ is a tool for the prediction of protonation states and pK of ionizable groups in macromolecular structures.

This content is being maintained by onufriev.

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tagsAMBER hydrogen hydrogen-ion concentration molecular dynamics Molecular modeling pK protonation

I2I-SiteEngineTool Content

http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/

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

Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.

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tagsalgorithms amino acids binding sites computational biology ligands macromolecular substances multiprotein complexes protein conformation protein interaction mapping proteins secondary protein structure

ICGEBnet Protein ToolsTool Content

http://www.icgeb.org/protein/

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

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.

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tagsalgorithms animals chemical models cluster analysis computational biology crystallography humans interferon alfa-2a molecular evolution molecular models molecular structure probability programming languages protein conformation protein databases protein folding protein interaction mapping proteins secondary protein structure sensitivity and specificity sequence homology serpins tertiary protein structure trypsin

ProFuncTool Content

http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/

Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.

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tagsbinding sites dna-binding proteins enzymes molecular models protein conformation protein sequence analysis proteins

SCRATCHTool Content

http://www.igb.uci.edu/servers/psss.html

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

SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.

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tagsdisulfides mutation protein conformation proteins secondary protein structure solvents 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

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

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

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

SiteEngineTool Content

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

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

SiteEngine is a server that searches protein structures for regions that can potentially function as binding sites by scanning for regions on the surface of one protein structure that resemble a specific binding site on the other.

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tagsamino acids binding sites chemical fractionation chondroitin lyases chromatography cultured cells dermatan sulfate fibroblasts glucuronates glucuronic acid glycosaminoglycans heparin lyase heparitin sulfate humans iduronic acid mammalian embryo molecular weight multiprotein complexes polyacrylamide gel electrophoresis polysaccharide-lyases protein conformation protein interaction mapping proteoglycans sulfates

SrideTool Content

http://sride.enzim.hu/

Protein > 3-D Structural Features

Sride is a tool for identificating stabilizing residues in protein structure.

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tagsamino acids conserved sequence hydrophobic and hydrophilic interactions molecular evolution molecular models pliability protein conformation protein folding proteins secondary protein structure temperature tertiary protein structure thermodynamics

pdbFunTool Content

http://pdbfun.uniroma2.it/

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

pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.

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tagsalgorithms amino acids protein conformation protein databases proteins systems integration time factors

Protein > 3-D Structure Comparison

CHC_FINDTool Content

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

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

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

EBI ToolsTool Content

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

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

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

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

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

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tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment transcription factors

PISCESTool Content

http://dunbrack.fccc.edu/pisces/

Protein > 3-D Structure Comparison
Protein > Sequence Retrieval

PISCES (Protein Sequence Culling Server) allows the user to weed out sequences from a set in order to obtain a subset of relatively high PDB structure quality and/or mutual sequence identity.

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tagsprotein conformation protein databases protein sequence analysis sequence alignment

SCR_FINDTool Content

http://schubert.bio.uniroma1.it/SCR_FIND/

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

SCR_FIND is a tool to analyze structurally conserved regions (SCRs) from superimposed structures and multiple sequence alignments.

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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

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

pdbFunTool Content

http://pdbfun.uniroma2.it/

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

pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.

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tagsalgorithms amino acids protein conformation protein databases proteins systems integration time factors

Protein > 3-D Structure Prediction

BhairPredTool Content

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

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

BhairPred is a tool for predicting beta-hairpins in protein sequences using a support vector machine.

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tagsalgorithms artificial intelligence neural networks (computer) protein sequence analysis secondary protein structure sequence alignment

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

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

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

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

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tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

FoldXTool Content

http://foldx.embl.de/

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.

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tagsmolecular structure mutation nucleic acid conformation protein conformation protein databases protein folding proteins single nucleotide polymorphism

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

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tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment transcription factors

I-Mutant2.0Tool Content

http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.

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tagsartificial intelligence point mutation protein engineering protein sequence analysis proteins tertiary protein structure thermodynamics

ICGEBnet Protein ToolsTool Content

http://www.icgeb.org/protein/

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

ICGEBnet Protein Tools is a resource for analysis of 3D protein structures including domain predictors, a protein fold similiarity server (PRIDE), and tools for calculating atom protusion (CX) and/or depth (DPX) indexes in 3D models.

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tagsalgorithms animals chemical models cluster analysis computational biology crystallography humans interferon alfa-2a molecular evolution molecular models molecular structure probability programming languages protein conformation protein databases protein folding protein interaction mapping proteins secondary protein structure sensitivity and specificity sequence homology serpins tertiary protein structure trypsin

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

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/

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

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase

SPACETool Content

http://ligin.weizmann.ac.il/space/

Protein > 3-D Structure Prediction

SPACE (Structure Prediction and Analysis based on Complementarity with Environment) is a suite of tools for predicting and analyzing structures of biomolecules and their complexes.

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tagsalgorithms amino acids automation bacterial proteins binding sites biotin computational biology factual databases formycins hydrogen bonding ligands molecular conformation molecular models molecular structure nucleic acids point mutation protein binding protein conformation protein databases proteins ribonucleotides ricin site-directed mutagenesis solvents streptavidin thermodynamics water x-ray crystallography

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

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

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

Protein > 3-D Structure Retrieval/Viewing

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

MRSTool Content

http://mrs.cmbi.ru.nl/

DNA > Sequence Retrieval and Submission
Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Retrieval

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.

This content is being maintained by maarten.

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tagsgenetic databases nucleic acid databases protein databases time factors

MovieMakerTool Content

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

Protein > 3-D Structure Retrieval/Viewing

MovieMaker is a web server that accepts PDB files or PDB accession numbers as input and allows short (~10 sec) downloadable movies to be generated of protein motions and interactions.

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tagsligands motion motion pictures as topic myoglobin protein folding proteins rotation vibration

PPGTool Content

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

Protein > 3-D Structure Retrieval/Viewing

The Protein Picture Generator (PPG) is a tool for making pictures (and animations) of protein structures from PDB files.

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tagsmolecular models protein conformation software design

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/

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

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

This content is being maintained by jompo.

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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase

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.

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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

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

GPCRsclassTool Content

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

Protein > Annotation and Function
Protein > Localization and Targeting

GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.

This content is being maintained by raghavagps.

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tagsadrenergic receptors artificial intelligence biogenic amine receptors cholinergic receptors dipeptides dopamine receptors g-protein-coupled receptors protein sequence analysis serotonin receptors

GRIFFINTool Content

http://griffin.cbrc.jp/

Protein > Annotation and Function

GRIFFIN (G-protein-Receptor Interacting Feature Finding INstrument) uses a support vector machine and hidden markov model to predict G-protein coupled receptors (GPCRs) and G-protein coupling selectivity.

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tagsartificial intelligence g-protein-coupled receptors heterotrimeric gtp-binding proteins ligands markov chains protein sequence analysis

InterProScanTool Content

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

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

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.

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tagsdatabase management systems dna sequence analysis humans protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

MEDockTool Content

http://medock.csie.ntu.edu.tw/

Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites.

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tagsalgorithms binding sites computer simulation dna drug design entropy ligands molecular models pharmaceutical preparations proteins

PEPVACTool Content

http://immunax.dfci.harvard.edu/PEPVAC/

Human Genome > Health and Disease
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

PEPVAC is a tool to assist in the development of multi-epitope vaccines. It is optimized for this task by predicting peptides with the ability to bind to several human leukocyte antigens that have similar peptide binding specificity.

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tagshla-a antigens hla-b antigens humans ligands peptides proteasome endopeptidase complex protein sequence analysis t-lymphocyte epitopes vaccines

ProFuncTool Content

http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/

Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.

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tagsbinding sites dna-binding proteins enzymes molecular models protein conformation protein sequence analysis proteins

ProTeusDatabase Content

http://www.proteus.cs.huji.ac.il/index.php

Protein > Annotation and Function
Protein > Domains and Motifs

ProTeus (Protein Terminus) is an archive of functional signatures in protein termini

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tagsoligopeptides protein databases protein sequence analysis protein sorting signals

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

WebGestaltTool Content

http://bioinfo.vanderbilt.edu/webgestalt/

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

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.

This content is being maintained by bzhang.

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tagsgene expression genes genetic databases genomics humans proteomics statistical data interpretation systems integration tissue distribution

Protein > Biochemical Features

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

DiANNATool Content

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

Protein > Biochemical Features
Protein > Sequence Features

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

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

H++Tool Content

http://biophysics.cs.vt.edu/H++

Protein > 3-D Structural Features
Protein > Biochemical Features

H++ is a tool for the prediction of protonation states and pK of ionizable groups in macromolecular structures.

This content is being maintained by onufriev.

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tagsAMBER hydrogen hydrogen-ion concentration molecular dynamics Molecular modeling pK protonation

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

PCETool Content

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

Protein > Biochemical Features

PCE (Protein Continuum Electrostatics) is an interface to electrostatic potentials and pKa calculations using the MEAD package.

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tagshydrogen-ion concentration molecular models muramidase proteins static electricity

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/

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

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

This content is being maintained by jompo.

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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase

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

WebProAnalystTool Content

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

Protein > Biochemical Features
Sequence Comparison > Analysis of Aligned Sequences

WebProAnalyst is a tool for searching for residues whose substitutions are correlated with variations in protein activity. Key physicochemical characteristics of these sites can be calculated.

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tagsantimicrobial cationic peptides proteins quantitative structure-activity relationship viral matrix proteins

Protein > Domains and Motifs

AUGUSTUSTool Content

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

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

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

This content is being maintained by Mario Stanke.

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

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

DIALTool Content

http://caps.ncbs.res.in/DIAL/home.html

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

DIAL (Domain Identification Algorithm) is a web server for the automatic identification of structural domains given the three-dimensional coordinates of a protein.

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tagsalgorithms amino acid motifs amino acid sequence amino acids aspartic acid endopeptidases calmodulin chemical models cluster analysis database management systems documentation factual databases hydroxymethylbilane synthase molecular models molecular sequence data molecular structure papain porins protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment tertiary protein structure x-ray crystallography

EBI ToolsTool Content

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

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

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

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

FF - Fragment FinderTool Content

http://cluster.physics.iisc.ernet.in/ff/

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

FF (Fragment Finder) takes a PDB ID, a structure coordinate file or a list of phi and psi angles as input and searches for matches to a specified structural fragment. Users can tailor the search based on sequence similarity and vary the dataset searched against.

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tagsamino acid motifs molecular structure proteins

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

GPSTool Content

http://csbl.bmb.uga.edu/~ffzhou/gps_web/

Protein > Domains and Motifs

Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.

This content is being maintained by ffzhou.

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tagsalgorithms amino acid sequence homology animals binding sites conserved sequence microfilament proteins nerve tissue proteins phosphoproteins phosphorylation protein binding protein kinases protein sequence analysis protein-serine-threonine kinases rats sequence alignment substrate specificity

InterProScanTool Content

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

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

InterProScan allows you to query using different protein signature recognition methods to look up InterPro annotations for your sequence. These annotations results often include gene ontology terms that you can associate with your sequence.

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tagsdatabase management systems dna sequence analysis humans protein databases protein sequence analysis proteins sequence alignment systems integration tertiary protein structure

KinasePhosTool Content

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

Protein > Domains and Motifs

KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences.

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tagscomputational biology markov chains phosphoproteins phosphorylation protein kinases protein sequence analysis

One-Block CYRCATool Content

http://bioinformatics.weizmann.ac.il/~milana/OneCYRCA/

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

One-Block CYRCA is a program for identifying blocks (local ungapped profiles of the most conserved regions of protein families and domains) in a multiple sequence alignment based on the LAMA and CYRCA block-to-block alignment methods.

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tagsadenosine triphosphatases algorithms amino acid motifs amino acid sequence amino acid sequence homology aspartylglucosylaminase automation binding sites catalysis computational biology conserved sequence dna nucleotidyltransferases dna-binding proteins endopeptidase clp enoyl-coa hydratase factual databases flavin-adenine dinucleotide gamma-glutamyltransferase helix-turn-helix motifs hydrolysis ligands molecular models protein binding protein databases protein folding protein sequence analysis proteins sequence alignment serine endopeptidases single-stranded dna structure-activity relationship tertiary protein structure transposases

PRODOCDatabase Content

http://hodgkin.mbu.iisc.ernet.in/~prodoc/

Protein > Domains and Motifs

PRODOC is a repository of domain assignments from Pfam for proteins encoded in different complete genomes and a tool for querying this information.

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tagsprotein databases protein sequence analysis proteins tertiary protein structure

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Protein > Domains and Motifs
RNA > Motifs

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

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tagsarabidopsis arabidopsis proteins dna sequence analysis peptides plant dna protein sequence analysis

PhyloDomeTool Content

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

Protein > Domains and Motifs
Protein > Phylogeny Reconstruction

PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.

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tagsanimals caenorhabditis elegans caenorhabditis elegans proteins drosophila proteins eukaryotic cells phylogeny protein sequence analysis proteins signal transduction tertiary protein structure

ProFuncTool Content

http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/

Protein > 3-D Structural Features
Protein > Annotation and Function
Protein > Domains and Motifs

ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.

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tagsbinding sites dna-binding proteins enzymes molecular models protein conformation protein sequence analysis proteins

ProTeusDatabase Content

http://www.proteus.cs.huji.ac.il/index.php

Protein > Annotation and Function
Protein > Domains and Motifs

ProTeus (Protein Terminus) is an archive of functional signatures in protein termini

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tagsoligopeptides protein databases protein sequence analysis protein sorting signals

QuasiMotiFinderTool Content

http://quasimotifinder.tau.ac.il/

Protein > Domains and Motifs

QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs).

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tagsamino acid motifs animals cattle conserved sequence furin logistic models molecular evolution protein sequence analysis sequence alignment

SCANMOTTool Content

http://caps.ncbs.res.in/scanmot/scanmot.html

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

SCANMOT is a sequence similarity searching tool that adds the additional constraints of simultaneous matching of multiple motifs.

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tagsalgorithms amino acid motifs amino acid sequence conserved sequence molecular evolution protein databases protein sequence analysis sequence alignment

SCRATCHTool Content

http://www.igb.uci.edu/servers/psss.html

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

SCRATCH is a suite of protein structure software and servers for the prediction of secondary structure, solvent accessibility, disulphide bridges, stability effects of single amino acid mutations, disordered regions, domains, beta-residue and beta-strand pairings, amino acid contact maps, and tertiary structure.

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tagsdisulfides mutation protein conformation proteins secondary protein structure solvents tertiary protein structure

SEARCHGTrTool Content

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

Other Molecules > Carbohydrates
Protein > Domains and Motifs

SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs.

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tagsanti-bacterial agents binding sites computational biology glycosylation glycosyltransferases metabolism protein conformation protein sequence analysis substrate specificity

Scooby-domainTool Content

http://ibivu.cs.vu.nl/programs/scoobywww/

Protein > Domains and Motifs

Scooby-domain (sequence hydrophobicity predicts domains) is a method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure.

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tagshydrophobic and hydrophilic interactions protein sequence analysis proteins tertiary protein structure

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

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

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

WebGestaltTool Content

http://bioinfo.vanderbilt.edu/webgestalt/

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

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.

This content is being maintained by bzhang.

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tagsgene expression genes genetic databases genomics humans proteomics statistical data interpretation systems integration tissue distribution

pdbFunTool Content

http://pdbfun.uniroma2.it/

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

pdbFun allows the user to search the PDB as a database of annotated residues. One can limit the search by annotations such as domains, binding sites, active sites, solvent exposure and residue type.

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tagsalgorithms amino acids protein conformation protein databases proteins systems integration time factors

Protein > Interactions, Pathways, Enzymes

ArrayXPathTool Content

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

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

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

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

BabelomicsTool Content

http://www.babelomics.org

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

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

This content is being maintained by juan_aguilar.

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

GenePath2Tool Content

http://www.genepath.org/genepath2

Protein > Interactions, Pathways, Enzymes

GenePath is a tool for automated construction of genetic networks and proposal of genetic experiments from mutant data.

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tagsanimals artificial intelligence caenorhabditis elegans computational biology dictyostelium dna dna mutational analysis dna sequence analysis expert systems gene expression regulation genes genetic epistasis genetic models genomics humans knowledge larva mutation neural networks (computer) research single-blind method

I2I-SiteEngineTool Content

http://bioinfo3d.cs.tau.ac.il/I2I-SiteEngine/

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

Interface-to-Interface (I2I)-SiteEngine compares pairs of interacting protein binding sites by recognizing similarity of physico-chemical properties and shapes in the protein-protein interfaces.

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tagsalgorithms amino acids binding sites computational biology ligands macromolecular substances multiprotein complexes protein conformation protein interaction mapping proteins secondary protein structure

Onto-ToolsTool Content

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

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

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

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

PEPVACTool Content

http://immunax.dfci.harvard.edu/PEPVAC/

Human Genome > Health and Disease
Protein > Annotation and Function
Protein > Interactions, Pathways, Enzymes

PEPVAC is a tool to assist in the development of multi-epitope vaccines. It is optimized for this task by predicting peptides with the ability to bind to several human leukocyte antigens that have similar peptide binding specificity.

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tagshla-a antigens hla-b antigens humans ligands peptides proteasome endopeptidase complex protein sequence analysis t-lymphocyte epitopes vaccines

POPSCOMPTool Content

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

Protein > Interactions, Pathways, Enzymes

POPSCOMP is a system for analysing the interaction between components of complexes based on calculations of the accessible surface that is buried when the complex is formed.

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tagsanti-bacterial agents dna macromolecular substances proteins ribosomes rna

PRISMTool Content

http://gordion.hpc.eng.ku.edu.tr/prism/

Protein > Interactions, Pathways, Enzymes

PRISM (PRotein Interactions by Structural Matching) is a tool for analysing protein interfaces and predicting protein-protein interactions.

This content is being maintained by agursoy.

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tagsalgorithms protein conformation protein interaction mapping

Pathway ExplorerTool Content

https://pathwayexplorer.genome.tugraz.at/

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

Pathway Explorer is a tool for visualizing high throughput expression data simultaneously with biological pathway data available from KEGG, BioCarta, and GenMAPP.

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tagsgene expression profiling genetic databases oligonucleotide array sequence analysis systems integration

Pathway extractionTool Content

http://rsat.bigre.ulb.ac.be/rsat/index_neat.html

Protein > Interactions, Pathways, Enzymes

The pathway extraction tool is a part of the network analysis tool suite (NeAT). Given a metabolic network, the tool extracts a subnetwork that connects a list of input compounds, reactions, EC numbers or enzyme-coding genes. Three metabolic networks (KEGG LIGAND, KEGG RPAIR and MetaCyc) are preloaded, but custom networks can be submitted as well.

This content is being maintained by karoline.

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tagsmetabolic networks metabolic pathway metabolism path finding pathfinding subnetwork subnetworks

SiteEngineTool Content

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

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

SiteEngine is a server that searches protein structures for regions that can potentially function as binding sites by scanning for regions on the surface of one protein structure that resemble a specific binding site on the other.

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tagsamino acids binding sites chemical fractionation chondroitin lyases chromatography cultured cells dermatan sulfate fibroblasts glucuronates glucuronic acid glycosaminoglycans heparin lyase heparitin sulfate humans iduronic acid mammalian embryo molecular weight multiprotein complexes polyacrylamide gel electrophoresis polysaccharide-lyases protein conformation protein interaction mapping proteoglycans sulfates

VisANTTool Content

http://visant.bu.edu/

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

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

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

WebGestaltTool Content

http://bioinfo.vanderbilt.edu/webgestalt/

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

WebGestalt (WEB-based GEne SeT AnaLysis Toolkit) is a system facilitating the analysis of sets of genes. Gene sets can be compared using set operations (intersection, union, etc.), different annotations can be selected and retrieved for the set, and sets can be visualized and organized by a user-selected method (Gene Ontology, chromosomal distribution, etc.). WebGestalt can also perform a statistical analysis to suggest areas of interest with respect to the set of genes selected.

This content is being maintained by bzhang.

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tagsgene expression genes genetic databases genomics humans proteomics statistical data interpretation systems integration tissue distribution

Protein > Localization and Targeting

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

GPCRsclassTool Content

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

Protein > Annotation and Function
Protein > Localization and Targeting

GPCRsclass is a tool for predicting amine-binding receptors based on a protein sequence provided by the user.

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tagsadrenergic receptors artificial intelligence biogenic amine receptors cholinergic receptors dipeptides dopamine receptors g-protein-coupled receptors protein sequence analysis serotonin receptors

Servers at University College LondonTool Content

http://bioinf.cs.ucl.ac.uk/web_servers/

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

A suite of tools that includes: PSIPRED, a protein structure prediction server; GenTHREADER, for genomic protein fold recognition; MEMSAT2, for transmembrane protein structure prediction; GTD, the genomic threading database; DISOPRED, a dynamic disorder prediction server; DomPred, a domain prediction server; and COPS, for the comparison of protein structure classifications. UCL web portal has been updated to include a fully automated 3-D modeling pipeline, BioSerf.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial genome computational biology database management systems documentation factual databases false positive reactions fungal genome gene expression profiling genetic databases genome genomics humans london mathematics membrane proteins molecular evolution molecular models molecular sequence data neural networks (computer) open reading frames peptide fragments polypyrimidine tract-binding protein probability protein conformation protein databases protein folding protein sequence analysis proteins proteome proteomics reproducibility of results secondary protein structure sensitivity and specificity sequence alignment sequence analysis sequence homology structural models tertiary protein structure theoretical models

TMBETA-NETTool Content

http://psfs.cbrc.jp/tmbeta-net/

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

Tool that predicts transmembrane beta strands in an outer membrane protein from its amino acid sequence.

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tagsalgorithms amino acid sequence amino acids bacterial outer membrane proteins cell membrane factual databases membrane proteins molecular models neural networks (computer) reproducibility of results secondary protein structure

TRAMPLETool Content

http://gpcr.biocomp.unibo.it/biodec/

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

TRAMPLE is a tool for the prediction of transmembrane helices, transmembrane strands, secondary structure, and signal peptides.

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tagsalgorithms amino acid sequence amino acid sequence homology animals bacterial outer membrane proteins biological models chemical models computer security computer simulation database management systems double-blind method escherichia coli evaluation studies as topic factual databases forecasting haemophilus influenzae humans markov chains membrane proteins molecular models molecular sequence data neural networks (computer) porins protein folding protein sequence analysis protein sorting signals reproducibility of results rhodopseudomonas secondary protein structure sequence alignment software design statistical models

Protein > Molecular Dynamics and Docking

FoldXTool Content

http://foldx.embl.de/

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

FOLD-X is a program for calculating the folding energies of proteins and for calculating the effect of a point mutation on the stability of a protein.

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tagsmolecular structure mutation nucleic acid conformation protein conformation protein databases protein folding proteins single nucleotide polymorphism

I-Mutant2.0Tool Content

http://gpcr2.biocomp.unibo.it/cgi/predictors/I-Mutant2.0/I-Mutant2.0.cgi

Protein > 3-D Structure Prediction
Protein > Molecular Dynamics and Docking

I-Mutant2.0 is a tool that can predict the effect of a single point mutation on protein stability from protein sequences or protein structures.

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tagsartificial intelligence point mutation protein engineering protein sequence analysis proteins tertiary protein structure thermodynamics

MEDockTool Content

http://medock.csie.ntu.edu.tw/

Protein > Annotation and Function
Protein > Molecular Dynamics and Docking

MEDock (Maximum-Entropy based Docking) is a tool for predicting ligand binding sites.

This content is being maintained by dirty.

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tagsalgorithms binding sites computer simulation dna drug design entropy ligands molecular models pharmaceutical preparations proteins

PatchDockTool Content

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

Protein > Molecular Dynamics and Docking

PatchDock is an algorithm for molecular docking. The input is two molecules of any type: proteins, DNA, peptides, drugs. The output is a list of potential complexes sorted by shape complementarity criteria.

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tagsalgorithms alpha-amylases antibodies antigen receptors bacterial proteins binding sites capsid proteins computational biology exotoxins influenza virus hemagglutinin glycoproteins ligands macromolecular substances membrane proteins molecular models multiprotein complexes phosphoenolpyruvate sugar phosphotransferase system protein conformation protein interaction mapping protein-serine-threonine kinases proteins secondary protein structure viral antigens

SymmDockTool Content

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

Protein > Molecular Dynamics and Docking

SymmDock is an server for prediction of complexes with cyclically symmetry by geometry based molecular docking.

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

Protein > Phylogeny Reconstruction

POWERTool Content

http://power.nhri.org.tw/

DNA > Phylogeny Reconstruction
Protein > Phylogeny Reconstruction

The Phylogenetic Web Repeater (POWER) allows users to perform phylogenetic analysis using the PHYLIP package. The POWER pipeline can start with processing either multiple sequence alignments (MSA) or can proceed directly with aligned sequences.

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tagsalgorithms dna sequence analysis phylogeny protein sequence analysis rna sequence analysis sequence alignment systems integration

PhyloDomeTool Content

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

Protein > Domains and Motifs
Protein > Phylogeny Reconstruction

PhyloDome is a tool with which you can visualize and analyze the phylogenetic distribution of one or more eukaryotic domains.

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tagsanimals caenorhabditis elegans caenorhabditis elegans proteins drosophila proteins eukaryotic cells phylogeny protein sequence analysis proteins signal transduction 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

Protein > Proteomics

DeNovoIDDatabase Content

http://proteomics.mcw.edu/denovoid/

Protein > Proteomics

DeNovoID is a tool for protein identification using de novo peptide sequence data from mass spectrometry experiments.

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tagsalgorithms amino acids mass spectrometry peptides protein databases protein sequence analysis proteomics

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

CBS DAS protein viewerTool Content

http://www.cbs.dtu.dk/cgi-bin/das

Human Genome > Annotations
Protein > 2-D Structure Prediction
Protein > 3-D Structure Retrieval/Viewing
Protein > Annotation and Function
Protein > Biochemical Features
Protein > Domains and Motifs
Protein > Localization and Targeting
Protein > Sequence Features

The CBS DAS protein viewer uses the distributed annotation system (DAS) to integrate and present annotation data from multiple sources for a protein sequence.

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tagsprotein sequence analysis systems integration

DiANNATool Content

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

Protein > Biochemical Features
Protein > Sequence Features

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

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

PcleavageTool Content

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

Protein > Sequence Features

Pcleavage is a tool that uses a support vector machine to predict immunoproteasome and constitutive proteasome cleavage sites in antigenic sequences.

This content is being maintained by raghavagps.

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tagsantigens artificial intelligence histocompatibility antigens class i ligands proteasome endopeptidase complex protein sequence analysis proteins

REPPERTool Content

http://protevo.eb.tuebingen.mpg.de/repper

Protein > Sequence Features

REPPER (REPeats and their PERiodicities) is a tool for detecting and analysing regions in protein sequences or sequence alignements that have short gapless repeats.

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tagsamino acid repetitive sequences bacterial adhesins protein sequence analysis proteins secondary protein structure sequence alignment

RPBSResource Content

http://bioserv.rpbs.jussieu.fr/

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

Ressource Parisienne en Bioinformatique Structurale (RPBS) is a structural bioinformatics resource with several types of specific services including tools for searching sequence (AUTOMAT) and structure (YAKUSA) databases and for homology modelling (WLOOP).

This content is being maintained by jompo.

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tagsacquired immunodeficiency syndrome algorithms amino acid sequence amino acid sequence homology amino acids animals arabidopsis autoimmune diseases azurin bacterial genome chemical models computational biology computer simulation computer-assisted numerical analysis consensus sequence database management systems dna dna sequence analysis evaluation studies as topic factual databases genetic databases globins glycine hiv humans hydrolases leghemoglobin logistic models methods molecular models molecular sequence data nucleic acid sequence homology plant genome plastocyanin protein conformation protein structural homology proteins rats reproducibility of results secondary protein structure sequence alignment sequence analysis sequence homology solvents thiosulfate sulfurtransferase

Protein > Sequence Retrieval

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

EBI ToolsTool Content

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

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

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

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

FeatureExtractTool Content

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

DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

MRSTool Content

http://mrs.cmbi.ru.nl/

DNA > Sequence Retrieval and Submission
Protein > 3-D Structure Retrieval/Viewing
Protein > Sequence Retrieval

MRS is a biological data retrieval system that can be accessed over the web, or installed and used locally. MRS indexes several flat-file data sets for searching, including EMBL nucleotide, UniProt, PDB and KEGG. Searches can be performed globally, or on one or more flat file fields per data set.

This content is being maintained by maarten.

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tagsgenetic databases nucleic acid databases protein databases time factors

PISCESTool Content

http://dunbrack.fccc.edu/pisces/

Protein > 3-D Structure Comparison
Protein > Sequence Retrieval

PISCES (Protein Sequence Culling Server) allows the user to weed out sequences from a set in order to obtain a subset of relatively high PDB structure quality and/or mutual sequence identity.

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tagsprotein conformation protein databases protein sequence analysis sequence alignment

RNA > Functional RNAs

MicroInspectorTool Content

http://bioinfo.uni-plovdiv.bg/microinspector/

Expression > Gene Regulation
RNA > Functional RNAs
RNA > Motifs

MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.

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tagsbase pairing binding sites messenger rna micrornas rna sequence analysis

miRUTool Content

http://bioinfo.noble.org/gateway/index.php?option=com_content&task=view&id=53&It...

Expression > Gene Regulation
RNA > Functional RNAs

miRU is a tool that takes as an input a small miRNA sequence and then searches for complementary matches in TIGR plant-specific gene data sets to predict potential target genes.

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tagsalgorithms base pair mismatch messenger rna micrornas plant genes plant rna rna sequence analysis

snoGPSTool Content

http://lowelab.ucsc.edu/snoGPS/

RNA > Functional RNAs

snoGPS allows you to search for H/ACA snoRNA (small nucleolar RNA) genes in a genomic sequence

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tagsalgorithms base sequence computational biology fungal genome fungal rna genomics guide rna molecular sequence data phylogeny pseudouridine ribosomal rna saccharomyces cerevisiae small nucleolar rna transfer rna

snoscanTool Content

http://lowelab.ucsc.edu/snoscan/

RNA > Functional RNAs

Snoscan allows you to search for C/D box methylation guide snoRNA (small nucleolar RNA) genes in a genomic sequence

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tagsalgorithms base pairing cell nucleolus fungal rna genetic models methylation ribose ribosomal rna saccharomyces cerevisiae small nuclear rna statistical models

tRNAscan-SETool Content

http://lowelab.ucsc.edu/tRNAscan-SE/

RNA > Functional RNAs

tRNAscan-SE allows you to search for tRNA genes in genomic sequence. (site hosted by Lowe Lab at UCSC)

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tagsanimals bacterial rna evaluation studies as topic factual databases genome genomics introns rna small nucleolar rna transfer rna

RNA > Motifs

FOLDALIGNTool Content

http://foldalign.ku.dk

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

FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.

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tagsalgorithms conserved sequence nucleic acid conformation nucleic acid sequence homology rna rna sequence analysis sequence alignment untranslated rna

MicroInspectorTool Content

http://bioinfo.uni-plovdiv.bg/microinspector/

Expression > Gene Regulation
RNA > Functional RNAs
RNA > Motifs

MicroInspector is a tool that detects miRNA (microRNA) binding sites in your input sequence by searching against databases of known miRNA binding sites.

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tagsbase pairing binding sites messenger rna micrornas rna sequence analysis

PatMatchTool Content

http://www.arabidopsis.org/cgi-bin/patmatch/nph-patmatch.pl

DNA > Structure and Sequence Feature Detection
Expression > Gene Regulation
Expression > cDNA, EST, SAGE
Protein > Domains and Motifs
RNA > Motifs

PatMatch is a pattern matching tool that allows you to search for short (<20 residues) nucleotide or peptide sequences and can accomodate ambiguous/degenerate patterns.

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tagsarabidopsis arabidopsis proteins dna sequence analysis peptides plant dna protein sequence analysis

RNA > Sequence Retrieval

EBI ToolsTool Content

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

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

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

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

FeatureExtractTool Content

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

DNA > Annotations
DNA > Sequence Retrieval and Submission
Human Genome > Annotations
Protein > Sequence Retrieval
RNA > Sequence Retrieval

The FeatureExtract server extracts sequence and feature annotations, such as intron/exon structure, from GenBank entries and other GenBank format files.

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tagschromosomes dna sequence analysis gene components humans nucleic acid databases

RNA > Structure Prediction, Visualization, and Design

DINAMeltTool Content

http://mfold.rna.albany.edu/?q=DINAMelt

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

DINAMelt is a tool for predicting hybridization and folding (secondary structure) of DNA and RNA using equilibrium thermodynamic methods.

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tagsalgorithms animals bacterial rna base sequence calorimetry dna dna sequence analysis fungal rna genetic hybridization introns molecular sequence data nucleic acid conformation nucleic acid denaturation nucleic acid hybridization oligonucleotides oligoribonucleotides phylogeny rats rna rna sequence analysis single-stranded dna structure-activity relationship temperature theoretical models transition temperature

E-RNAiTool Content

http://e-rnai.dkfz.de/

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

E-RNAi is a tool for designing and evaluating dsRNA constructs suitable for RNAi experiments in 12 organisms including Drosophila, C. elegans, human and other emerging model organisms. E-RNAi also facilitates the design of secondary RNAi reagents for validation experiments, evaluation of pooled siRNA reagents and batch design.

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tagsanimals apoptosis caenorhabditis elegans cell cycle cell survival computational biology core binding factor alpha 2 subunit cultured cells dna primers dna-binding proteins double-stranded rna drosophila melanogaster drosophila proteins essential genes gene knockdown techniques genome genomic library genomics humans indicators and reagents inhibitor of apoptosis proteins insect genes phenotype proteome proto-oncogene proteins reproducibility of results rna interference rna sequence analysis sequence homology small interfering rna transcription factors

FOLDALIGNTool Content

http://foldalign.ku.dk

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

FOLDALIGN is an algorithm for local simultaneous folding and aligning two or more RNA sequences.

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tagsalgorithms conserved sequence nucleic acid conformation nucleic acid sequence homology rna rna sequence analysis sequence alignment untranslated rna

KinefoldTool Content

http://kinefold.u-strasbg.fr/

RNA > Structure Prediction, Visualization, and Design

Kinefold calculates (and animates) the folding kinetics of RNA sequences including pseudoknots.

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tagsalgorithms computer simulation dna dna sequence analysis nucleic acid conformation rna rna sequence analysis

RNALOSSTool Content

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

RNA > Structure Prediction, Visualization, and Design

RNALOSS (RNA locally optimal secondary structure) is a tool for the computation of locally optimal secondary structures.

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tagsalgorithms nucleic acid conformation rna rna sequence analysis

Sequence Comparison > Alignment Editing and Visualization

CHAOS/DIALIGN WWW serverTool Content

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

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

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

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

enoLOGOSTool Content

http://biodev.hgen.pitt.edu/enologos/

Sequence Comparison > Alignment Editing and Visualization

enoLOGOS creates sequence logos based on a variety of input, including sequence alignments, probability and alignment matrices and energy measurements.

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tagsamino acids binding sites dna sequence analysis dna-binding proteins sequence alignment zinc fingers

Sequence Comparison > Analysis of Aligned Sequences

CAMPOTool Content

http://schubert.bio.uniroma1.it/CAMPO/index.html

Sequence Comparison > Analysis of Aligned Sequences

CAMPO is a tool to analyze conserved regions from a multiple sequence alignment

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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

CHC_FINDTool Content

http://schubert.bio.uniroma1.it/CHC_FIND/index.html

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

CHC_FIND is a tool to analyze conserved hydrophobic contacts (CHC) from multiple structural alignments. In addition to a multiple sequence alignment, a structural alignment which provides the superposition of structurally conserved regions (SCRs) (i.e., results from SCR_FIND) needs to be provided.

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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

ConSurfTool Content

http://consurf.tau.ac.il/

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

The ConSurf server allows one to map levels of amino acid conservation to known protein structures in order to study areas of potential functional importance on the surface of the protein. A PDB file is required as input, and a multiple sequence alignment is optional. If an alignment is not provided, ConSurf will build one by performing a search for homologous sequences and then aligning them. ConSurf 2010 combines ConSurf and ConSeq for an easier, more intuitive interface.

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tagsamino acid sequence amino acid sequence homology amino acid substitution amino acids bacterial proteins base sequence bayes theorem bcl-x protein conserved sequence molecular evolution molecular models nucleic acid conformation phylogeny potassium channels protein conformation protein databases protein sequence analysis proteins proto-oncogene proteins c-bcl-2 sequence alignment sequence analysis

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

MaMTool Content

http://compbio.cs.sfu.ca/MAM.htm

Sequence Comparison > Analysis of Aligned Sequences

The Multiple alignment Manipulator (MaM) takes a multiple alignment of genomic sequences as input and calculates the locations of exons, common repeat elements and unique regions based on user-selected programs/information. The graphical display also allows users to focus an assessment of sequence variation on the identified regions.

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tagsexons genomics nucleic acid repetitive sequences phylogeny sequence alignment

One-Block CYRCATool Content

http://bioinformatics.weizmann.ac.il/~milana/OneCYRCA/

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

One-Block CYRCA is a program for identifying blocks (local ungapped profiles of the most conserved regions of protein families and domains) in a multiple sequence alignment based on the LAMA and CYRCA block-to-block alignment methods.

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tagsadenosine triphosphatases algorithms amino acid motifs amino acid sequence amino acid sequence homology aspartylglucosylaminase automation binding sites catalysis computational biology conserved sequence dna nucleotidyltransferases dna-binding proteins endopeptidase clp enoyl-coa hydratase factual databases flavin-adenine dinucleotide gamma-glutamyltransferase helix-turn-helix motifs hydrolysis ligands molecular models protein binding protein databases protein folding protein sequence analysis proteins sequence alignment serine endopeptidases single-stranded dna structure-activity relationship tertiary protein structure transposases

PriFiTool Content

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

DNA > Tools For the Bench
Sequence Comparison > Analysis of Aligned Sequences

PriFi is a tool for designing and evaluating primer pairs based on the input of a DNA sequence alignment; useful for the PCR amplification of homologs.

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tagsdna primers genomics nucleic acid sequence homology phylogeny polymerase chain reaction sequence alignment

SCR_FINDTool Content

http://schubert.bio.uniroma1.it/SCR_FIND/

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

SCR_FIND is a tool to analyze structurally conserved regions (SCRs) from superimposed structures and multiple sequence alignments.

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tagscomputational biology hydrophobic and hydrophilic interactions molecular evolution molecular models potassium channels protein conformation proteins trypsin inhibitors

WebProAnalystTool Content

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

Protein > Biochemical Features
Sequence Comparison > Analysis of Aligned Sequences

WebProAnalyst is a tool for searching for residues whose substitutions are correlated with variations in protein activity. Key physicochemical characteristics of these sites can be calculated.

NAR Web Server Issue 2005
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tagsantimicrobial cationic peptides proteins quantitative structure-activity relationship viral matrix proteins

Sequence Comparison > Comparative Genomics

CisMolsTool Content

http://cismols.cchmc.org/

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

CisMols (Cis-regulatory Modules) is a tool that identifies compositionally predicted cis-clusters that occur in groups of co-regulated genes within each of their ortholog-pair evolutionarily conserved cis-regulatory regions.

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tagsbase sequence binding sites conserved sequence gene expression regulation genomics response elements transcription factors

DCODE.ORGResource Content

http://www.dcode.org/

Human Genome > Other Resources
Sequence Comparison > Comparative Genomics

The dcode.org website provides access to tools for comparative genomic analyses developed by the Comparative Genomics Center at the Lawerence Livermore National Laboratory. Tools include: zPicture, Mulan, eShadow, rVista, CREME, and the ECR Browser.

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tagsbase sequence binding sites computational biology gene expression regulation genetic promoter regions genomics humans molecular evolution nucleic acid regulatory sequences phylogeny sequence alignment transcription factors

MLSTTool Content

http://www.mlst.net/

DNA > Phylogeny Reconstruction
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

MLST (Multi Locus Sequence Typing) is a nucleotide sequence based approach for the unambiguous characterisation of isolates of bacteria and other organisms using the sequences of internal fragments of seven house-keeping genes.

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tagsalleles bacteria bacterial dna bacterial genes bacterial meningitis bacterial typing techniques cerebrospinal fluid cluster analysis dna sequence analysis evaluation studies as topic gene frequency humans meningococcal infections molecular sequence data mycological typing techniques neisseria meningitidis nucleic acid databases pneumococcal meningitis polymerase chain reaction serotyping streptococcus pneumoniae virulence

Projector 2Tool Content

http://molgen.biol.rug.nl/websoftware/projector2/

DNA > Mapping and Assembly
Model Organisms > Microbes
Sequence Comparison > Comparative Genomics

Projector 2 allows users to map completed portions of the genome sequence of an organism onto the finished (or unfinished) genome of a closely-related species or strain. Using the related genome sequence as a template can facilitate sequence assembly and the sequencing of the remaining gaps.

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tagsalgorithms bacterial genome contig mapping dna primers genomics polymerase chain reaction

Sequence Comparison > Multiple Sequence Alignments

CHAOS/DIALIGN WWW serverTool Content

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

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

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

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

EBI ToolsTool Content

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

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

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

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

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

NAR Web Server Issue 2005NAR Web Server Issue 2011
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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

PRALINETool Content

http://ibivu.cs.vu.nl/programs/pralinewww/

Protein > 2-D Structure Prediction
Sequence Comparison > Multiple Sequence Alignments

Praline is a multiple sequence alignment program that can integrate information from sequence similarity searches and secondary structure prediction.

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tagsacid anhydride hydrolases algorithms amino acid motifs amino acid sequence amino acid sequence homology amino acids bacterial proteins binding sites cluster analysis computational biology consensus sequence cytochrome p-450 enzyme system database management systems discriminant analysis flavodoxin genetic databases hiv integrase membrane proteins molecular models molecular sequence data neural networks (computer) protein conformation protein databases protein folding protein sequence analysis proteins reproducibility of results secondary protein structure sensitivity and specificity sequence alignment systems integration tertiary protein structure

Sequence Comparison > Pairwise Sequence Alignments

FFASTool Content

http://ffas.godziklab.org

Protein > 3-D Structure Prediction
Protein > Domains and Motifs
Sequence Comparison > Analysis of Aligned Sequences
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Pairwise Sequence Alignments

The Fold & Function Assignment System (FFAS) takes an amino-acid sequence as input and generates a profile which is compared to several sets of sequence profiles including PDB, SCOP, and PFAM. Public metagenomic sequence data has been added to FFAS, so that the profile of a user's protein can be compared to 20 additional profile databases including several complete proteomes, etc.

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tagsalgorithms amino acid sequence homology protein databases protein folding sequence alignment

ParAlignTool Content

http://www.paralign.org/

Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

ParAlign provides a service for sequence similarity searching powered by parallel computing technology. The two comparison algorithms used are Smith-Waterman and ParAlign (a heuristic method for sequence alignment).

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tagsalgorithms amino acid sequence homology computational biology computing methodologies factual databases microcomputers nucleic acid databases nucleic acid sequence homology protein databases sensitivity and specificity sequence alignment time factors

YASSTool Content

http://bioinfo.lifl.fr/yass/

Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

YASS performs local alignments of DNA sequences. It is available through a web interface and as a standalone command-line tool.

This content is being maintained by laurent.

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tagsalgorithms dna sequence analysis genomics nucleic acid sequence homology sequence alignment

Sequence Comparison > Similarity Searching

EBI ToolsTool Content

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

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

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

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

HHpredTool Content

http://protevo.eb.tuebingen.mpg.de/hhpred

Protein > 3-D Structure Comparison
Protein > 3-D Structure Prediction
Sequence Comparison > Similarity Searching

Based on the comparison of profile HMMs, HHpred takes a protein sequence or multiple sequence alignment as input and searches for remote homologues in an assortment of databases such as PDB, SMART and Pfam. The user can select either a local or global alignment method, and the search results can be used to generate 3D structural models.

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tagsamino acid sequence homology bacterial proteins markov chains protein conformation protein databases protein sequence analysis sequence alignment 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

ParAlignTool Content

http://www.paralign.org/

Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

ParAlign provides a service for sequence similarity searching powered by parallel computing technology. The two comparison algorithms used are Smith-Waterman and ParAlign (a heuristic method for sequence alignment).

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tagsalgorithms amino acid sequence homology computational biology computing methodologies factual databases microcomputers nucleic acid databases nucleic acid sequence homology protein databases sensitivity and specificity sequence alignment time factors

SCANMOTTool Content

http://caps.ncbs.res.in/scanmot/scanmot.html

Protein > Domains and Motifs
Sequence Comparison > Similarity Searching

SCANMOT is a sequence similarity searching tool that adds the additional constraints of simultaneous matching of multiple motifs.

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tagsalgorithms amino acid motifs amino acid sequence conserved sequence molecular evolution protein databases protein sequence analysis sequence alignment

YASSTool Content

http://bioinfo.lifl.fr/yass/

Sequence Comparison > Pairwise Sequence Alignments
Sequence Comparison > Similarity Searching

YASS performs local alignments of DNA sequences. It is available through a web interface and as a standalone command-line tool.

This content is being maintained by laurent.

NAR Web Server Issue 2005
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tagsalgorithms dna sequence analysis genomics nucleic acid sequence homology sequence alignment