On line analysis tools
English version of ABIM : Logiciels en ligne
- Search a sequence database
- Nucleic acids sequences
- Patterns (proteins)
- Prediction on protein sequences
- Alignments - Phylogeny
- Analysis tools package
- Sequence comparison
- BLAST (results with links Databases : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
- NCBI [E]
Databases : NR, Month, SwissProt, Dbest, DBSTS, PDB, Vector, Kabat, Mito, Alu, EpD, Yeast
- ProtEST -Protein matches for ESTs (BLASTX with -e 1e-6) NCBI
- BCM Proteins, nucleic acids [D, E, R, S]
- Expasy : blast at NCBI [D] with extra : analyse and align all HSPs
- IBB (Padoue)
- IGHM (French) [D]
Databases : NR, Month, SwissProt, Dbest, DBSTS, GBxxx, PDB, Vector, Kabat, NRSub, Transfac ...
- Strasbourg (Ballast : explore the depths of Blast searches) (French)
- TBI (Germany) [E, P]
- Toulouse (French)
- Organism-Specific Blast NCBI, another link
- Search of Anopheles gambiae NCBI (USA)
- Search of Aspergillus nidulans Oklahoma (USA)
- Search of Complete Genomes (E.C, S.C, M.J, M.G, B.S) BMERC (Blastp, Blastx) (USA)
- Search of CDD (Conserved Domain Database : rpsblast) NCBI (USA), see also Toulouse (French)
- Search of Dictyostelium (blastn) : Jena (Germany)
- Search of Drosophila : BDGP (Berkeley) [E]
- Search of EST (Human, Drosophila, Mouse, EMBLEsT..) EMBL (Germany)
- Search of E. Coli : Pasteur (French)
- Search of E. Coli : Birmingham (UK)
- Search of ESTHER (cholinesterase) INRA (French)
- Search of Fugu NCBI (USA)
- Search of HIV-1 (subtyping) NCBI (USA)
- Search of HIV Washington (USA)
- Search of Human Sanger (UK), see also NCBI (USA)
- Search of Human MIPS (blastn), see alos cDNA, see also EST (Germany)
- Search of Human UCSC (USA) (BLAT, not Blast)
- Search of Human Repeat Oklahoma (USA)
- Search of "Kegg genome" Kyoto (Japan)
- Search of Immunoglobulins NCBI (USA)
- Search of microbial genomes NCBI (USA)
- Multiple Custom Databases (P.falciparum, P.vivax, P.berghei, P. chabaudi, EST) NCBI (USA)
- Search of Neisseria gonorrhoeae Oklahoma (USA)
- Search of P450, UGT, cytochrome b5 Biobase (Denmark)
- Search of Plant knockout databases SDSC (USA)
- Search of P. falciparum NCBI
- Search of protein Databank PBIL (French) [S]
- Search of Streptococcus pyogenes Oklahoma (USA)
- Search of UTR Bari (Italy)
- Search of Zebra fish NCBI (USA)
- Species-Specific Protein Sequence Searches BCM (USA)
- PRINTS Blast Manchester (UK)
- Search of SBASE8.0 Database ICGEB (Italy)
- BEAUTY and BEAUTYX at BCM (BLAST Enhanced Alignment Utility : options CRSeq, CROS, Domain) ADN, Proteins (info) [D, E, R, S] et alignment for each "cluster"
- With Entrez and SRS Links BCM [D, E, R, S]
- Search of NRL_3D PBIL (French) [S]
- Search of Ex-NRL-3D (SWISS-MODEL Blast) Expasy
- Search of Ribosomal RNA (SSU, LSU) Gent (Belgium)
- Gapped BLAST (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
- MEGABLAST : Nucleotide (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
- PHI(Pattern Hit Initiated)-BLAST (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S)
- PSI(Postion Specific Iterated)-BLAST (résultats avec liens Banques : D, Entrez : E, Related Sequences : R, SRS : S)
- CMBI D
- NCBI [E]
- Pasteur [D]
- Toulouse [D]
- Search of NRL_3D or SwissProt PBIL (French) [S]
- Search of microorganisms U-ParisSud (French)
- Search of protein Databank PBIL (French) [S]
- SAWTED (Structure Assignment With Text Description) BMM (UK)
- BLAST2 or WU-BLAST2 (results with links Databases : D, Entrez : E, Related Sequences : R, SRS : S, Prosite : P)
- + BEAUTY : BCM Search Launcher Proteins, Nucleic acids [D, E, R, S]
- Cambridge (UK)
- EBI (UK) [D] (WU and Blast2)
- EMBL (Germany) [D] (WU)
- EMBNet [D]
- Submission form to the BLAST2 server at Lausanne at Expasy (Switzerland) [D], another link
- EMBNet (Switzerland) [D]
- GenomeNet (Japan) [D]
- Manchester (UK)
- Moscou (Russia)
- Pasteur, advanced form [D]
- Sanger (Blast and Ssaha : search on a set of protein or nucleotide databases available at the Sanger Centre)
- Wash-U. multi-processors Pasteur [D]
- Orthologue Blast2 (Finding orthologues & Distinguishing them from paralogues) Heidelberg (Germany)
- Search of Arabidopsis TAIR [D, E]
- Search of Arabidopsis (WU-Blast) TAIR (USA) [D, E]
- Search of ASD (Alternative Splicing Database) EBI (UK)
- Search of Bordetella Sanger (UK)
- Search of C. elegans DatabaseSanger (UK)
- Search of C. albicans DatabaseSanger (UK)
- Search of DOTS (Human and Mouse Transcribed Sequences) Allgenes (USA)
- Search of EST (EuroGeneIndexes) RBI (UK)
- Search of Drosophila (cosmids) Sanger (UK)
- Search of Dictyostelium Jena (Germany)
- Search of E. Coli : Pasteur (French)
- Search of EpoDB CBIL (USA) [D]
- Search of Ensembl CMBI (The Netherlands)
- Search of Fugu Ensembl
- Search of Haemophilus influenzae LANL (USA)
- Search of Human (selection of chromosomes) CMBI (The Netherlands)
- Search of Human Ensembl
- Search of Leishmania major Database Sanger (UK)
- Search of M. leprae Sanger (UK)
- Search of M. tuberculosis Sanger (UK)
- Search of Merops(protease database) Sanger (UK)
- Search of Mouse Jackson (USA)
- Search of Mouse Ensembl
- Search of Parasites EBI (UK)
- Search of P. falciparum Sanger (UK), see also NCBI (USA)
- Search of S. cerevisiae MIPS (Germany)
- Search of S. cerevisiae Stanford (USA) [D, E]
- Search of S. pombe Sanger (UK)
- Search of Salmonella typhi Sanger (UK)
- Search of Y. pestis Sanger (UK)
- Search of Zebrafish Ensembl
- Search of microbial genomes Sanger (follow the organism link) (UK)
- Search of TIGR Unique Gene Indices TIGR (USA)
- Search of UniProt EBI UK, see also PIR
- BLITZ
- FASTA
- Fasta3 CMBI (Netherlands)
- Fasta33 EBI (UK)
- Fasta33 Genomes EBI (UK)
- Fasta3 (TFASTX/TFASTY, FASTF/TFASTF, FASTS/TFASTS) Virginia (USA)
- GenomeNet (Japan)
- IGHM (French)
- DDBJ NIG (Japan)
- Fasta 3 Pasteur (French), advanced
- TBI (Germany)
- Search of PIR PIR (USA)
- Search of Arabidopsis TAIR (fasta 3)
- Search of HGBASE (European SNP database : fasta3) EBI (UK)
- Search of E. Coli Pasteur (French)
- Search of LGIC (Ligand Gated Ion Channel Database) EBI (UK)
- Search of PLACE (Plant Cis-acting Regulatory DNA Elements) DISC (Japan)
- Search of S. cerevisiae Stanford (USA)
- Species-Specific Protein Sequence Searches BCM (USA)
- Search of NRL_3D or SwissProt PBIL (French)
- Indiana (selection of nucleic genomic subset or selection of nucleic or proteic subset by keyword (SRS system) available)
- Needleman and Wunsch
- AbCheck UCL (London) test an antibody sequence against the Kabat sequence database
- ParAlign
- Search DNA and Protein Databases for Sequence Similarities (a.a. query sequence) Oslo (Norway)
- ProClust : Protein Clustering - Searching for Homologue Proteins by using transitivity
- RedHom (CPH models : finds a subset with low sequence similarity)
- Smith et Waterman
- Affine Smith-Waterman Algorithm Stanford (USA)
- FDF-SW Server (Fast Data Finder) EMBNet, see also GeneMatcher EMBNet
- MPsrch EBI (UK)
- Search DNA and Protein Databases for Sequence Similarities (a.a. query sequence) Oslo (Norway)
- SAMBA (Systolic Accelerator for Molecular Biological Applications) IRISA (French)
- SCANPS (Protein Databases) EBI
- PepPepSearch (Search of SWISS-PROT) ETH Zurich
- SSEARCH IGHM, see also PBIL
- SWsrch Search Service NIAS (Japan)
- SSAHA (Sequence Search and Alignment by Hashing Algorithm)
- Wise
- Protein/genomic or Protein/cDNA Pasteur (French)
- Protein vs genomic Sanger (UK)
- From a given aminoacids composition
- AAC
- Entered composition and search SWISS-PROT Expasy (results by e-mail)
- From a sequence of SWISS-PROT and search SWISS-PROT Expasy (results by e-mail)
- MultiIdent (aa, pI, MW, sequence tag and peptide mass fingerprinting data) Expasy
- PROPSEARCH
- From peptides obtained by enzymatic cleavage
- Aldente (tool to identify proteins from peptide mass fingerprinting data) Expasy
- Mapper Manchester (UK)
- MassDynSearch (searching SwissProt by protein mass after C or N-terminal digestion) ETHZ (Switzerland)
- MassSearch (searching SwissProt or EMBL by protein mass after digestion) ETHZ (Switzerland)
- MS-Fit, Tag, Edman (search GenPept, SwissProt, Owl) UCSF, see also UCSF-MSF
- MultiIdent (aa, pI, MW, sequence tag and peptide mass fingerprinting data) Expasy
- PeptideSearch EMBL
- PepSeeker (a database of proteome peptide identifications for investigating fragmentation patterns) Manchester (UK)
- Popitam (protein identification and characterization using tandem mass spectrometry data) Expasy (Switzerland)
- ProSight PTM 2.0 (improved protein identification and characterization for top down mass spectrometry) Illinois (USA)
- Protein identification (ProFound : OWL and PepFrag : GenPept, NRL-2D, PIR, Swiss-Prot) Rockfeller (USA)
- From pI and molecular mass
- MultiIdent (aa, pI, MW, sequence tag and peptide mass fingerprinting data) Expasy
- PeptIdent (pI, Mw and peptide mass fingerprinting data) Expasy
- TagIdent (and matching a short sequence tag of up to 6 amino acids) Expasy (formely Guess-Prot)
- From a nucleic acids sequence
- NuclPepSearch ETHZ (search SWISS-PROT)
- From a 3D structure
- 3D-PSSM (Protein Fold Recognition (former Foldfit)) BMM (UK)
- The DALI server EBI : search PDB (directly or by e-mail)
- Finding 3-D Similarities in Protein Structures SDSC (USA)
- SAWTED (Structure Assignment With Text Description) BMM (UK)
- VAST (Vector Alignment Search Tool) NCBI (USA)
- WWW server (SPASM, DEJAVU, MOLEMAN2) Uppsala (Sweden)
- Search Databases for a pattern
- Search protein databases
- Arabidopsis pattern matching TAIR
- AutoSCOP (automated prediction of SCOP classifications using unique pattern-class mappings) Munich (Germany)
- (See BCM Launcher) BLASTPAT et FASTPAT serach a pattern database derived from "Entrez" an alignment program (PIMA) : documentation
- Cognitor (Compare your sequence to COG database) NCBI (USA)
- Domain Fishing (a first step in protein comparative modelling) BML (UK)
- Halfwise (compare your DNA sequence against the whole of Pfam) Sanger (UK)
- HMMSearch (SwissProt, NPS) PBIL (French)
- HMM search in Pfam-A (Search the Pfam database by Hidden Markov models) Sanger, see also Washington
- HMM Query (Search PDB or/and SCOP) UCSC (USA)
- HMMER Pasteur (French)
- HMMER2 Pasteur (French)
- InterProScan (protein domains identifier) EBI (UK)
- Kangaroo (pattern search with regular expression) BluePrint
- Metamotif Search ISREC (Switzerland), see also Motif relation
- MOTIF Kyoto (Japan)
- NAIL (Network Analysis Interface for Linking HMMER results) EMBL (Germany)
- PATOSEQ (motif search and alignment program) Expasy
- Pattern Search : SwissProt - GenPept (ISREC) Pattern will be written with the Prosite syntax
- Pattern Match (PIR, NRL_3D, ProClass, PATCHX, FAMBASE) PIR (USA)
- PattinProt (Swissprot, NRL_3D, SP-TREMBL) PBIL (French)
- ScanProsite tool (Expasy) : SwissProt Pattern will be written according the syntax of Prosite
- Screening pattern or alignment Moscow (Russia)
- SledgeHMMER (searching the Pfam database) Albany (USA)
- SIR (provides the ability to simultaneously search a protein database with a sequence motif pattern and keywords) EMBL (Germany)
- Kangaroo (pattern search with regular expression) BluePrint
- MAST (Motif Alignment and Search Tool) San Diego (see next MEME), see also Pasteur
- PatMatch (Yeast Genome Pattern Matching) Stanford (USA)
- PatScan Argonne (Proteins or Nucleic acids, selection of genomic libraries)
- REPATT & TRANSPO (exact consecutive repeats - transposons) Barcelona (Spain)
- Search for Sequence Pattern (DNA) PBIL (French)
- Sig (Multiple Prosite motifs searching) Pasteur (French)
- Signal Scan (search TDF and Transfac for eucaryotic signal) : NIH, or search IMD NIH
- STAn (looking for nucleotidic and peptidic patterns in chromosomes) Rennes (French)
- Sequence Assembly
- CAP (Contig Assembly Program Based on Sensitive Detection of Fragment Overlaps) IFOM (Italy)
- CAP3 PBIL (Fr
- EGassembler (large-scale processing, clustering and assembling ESTs and genomic DNA fragments) Kyoto (Japan)
- ESSEM (Est's aSSEmbly using Malig) LSI (Spain)
- Gene Recognition and Assembly (GRAIL) ORNL (USA)
- MERGER (merge two overlapping sequences) Pasteur (French)
- Content - Codon usage - ...
- Codontree (codon usage table, distance matrix and bases composition) Pasteur (USA)
- Codon Usage Tabulated from GenBank CUTG (Japan) compilation by organism, see also Countcodon (for a sequence)
- CodonO (codon usage bias analysis within and across genomes) Miami (USA)
- Codonw (Correspondence Analysis of Codon Usage) Pasteur (French)
- CorGen (measuring and generating long-range correlations for DNA sequence analysis) Berlin (Germany)
- Countcodon Kazusa (Japan)
- CpG islands bioinformatics, see also EBI (UK), see also Iowa (USA)
- CpG rich regions Pasteur, see also plot, see also newcpgseek
- DSHIFT (for predicting DNA chemical shifts) Shatin (Hong Kong)
- EMBOSS at Pasteur (French), see also EMBOSS at CBRG (UK)
- Create a codon usage table CUSP
- Codon usage statistics CHIPS
- Codon usage table comparison CODCMP
- Find differences (SNPs) between nearly identical sequences DIFFSEQ
- Displays a non-overlapping wordmatch dotplot of two sequences DOTPATH
- Displays a wordmatch dotplot of two sequences DOTTUP
- Draws circular maps of DNA constructs CIRDNA
- Draws linear maps of DNA constructs LINDNA
- Synonymous codon usage Gribskov statistic plot SYCO
- Protein pattern search after translation FUZZTRAN
- Calculates the fractional GC content of a nucleic acid sequence GEECEE
- FeatureScan (revealing property-dependent similarity of nucleotide sequences) Braunschweig (Germany)
- Find the linguistic complexity in nucleotide sequences COMPLEX
- Finds MAR/SAR sites in nucleic sequences MARSCAN
- Searches DNA sequences for matches with primer pairs PRIMERSEARCH
- Counts words of a specified size in a DNA sequence WORDCOUNT
- Residue/base frequency table or plot FREAK
- Display a sequence with restriction cut sites, translation etc REMAP
- Silent mutation restriction enzyme scan SILENT
- Reverse and complement a sequence REVSEQ
- Wobble base plot WOBBLE
- GC-Profile (tool for visualizing and analyzing the variation of GC content in genomic sequences) Tianjin (China)
- GCUA (Graphical Codon Usage Analyser) Regensburg (Germany)
- GenDecoder (genetic code prediction for metazoan mitochondria) Vigo (Spain)
- JCat (to adapt codon usage of a target gene to its potential expression host) Braunschweig (Germany)
- MSBAR (mutate sequence beyond all recognition) Pasteur (French)
- OPTIMIZER (optimizing the codon usage of DNA sequences) Tarragona (Spain)
- Riche en ... (graphical display of content in selected bases) ABIM (in french)
- REPK (to select restriction endonucleases for terminal restriction fragment length polymorphism analysis) Washington (USA)
- Verbumculus ( over- or under-represented words : suffixe tree) California (USA)
- Map (restriction)
- Arabidopsis Restriction Mapper TAIR (USA)
- NEBcutter V2.0 BioLabs
- TACG Pasteur (French), see also California (USA)
- Webcutter Yale, mirror at Sweden
- Restenzyme Budapest (Hungary)
- RESTRICT (finds restriction enzyme cleavage sites) Pasteur (French)
- Restriction Mapper
- Restriction Site Analysis UMMS (USA)
- RIFLE (16S rDNA-based identification of microorganisms by comparison with RDP database restriction patterns) Bielefeld (Germany)
- WatCut (Cleave your DNA online, and create new cleavage sites in your oligos using silent mutations) Waterloo (Canada)
- Yeast Genome Restriction Analysis Stanford, see also Reverse Restricion Mapping (USA)
- Microarray - Genomics
- ACID (database for microarray clone information) Lund (Sweden)
- Adaptive quality-based clustering of gene expression profiles Sista (Belgium)
- ADGO (analysis of differentially expressed gene sets using composite GO annotation) Daejeon (Korea)
- Affycomp (benchmark for Affymetrix GeneChip expression measures) Johns Hopkins (USA)
- AMPhora Expression Data Analysis MIPS (Germany)
- ANOVA (NIA array analysis tools) NIH (USA)
- Arabidopsis Co-expression Tool (ACT) (tools for microarray-based gene expression analysis) Leeds (UK)
- ArrayCyGHt (analysis and visualization of array-CGH data) Seoul (Korea)
- ArrayFusion (application for multi-dimensional analysis of CGH, SNP and microarray data) Taipei (Taiwan)
- ArrayPipe (a flexible processing pipeline for microarray data) Vancouver (Canada)
- ArrayXPath (mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics) Seoul (Korea)
- Asterias (data normalization to aCGH analysis, molecular signatures with survival data, ..) CNIO (Spain)
- CAPweb (a bioinformatics CGH array Analysis Platform) Paris (French)
- CARMAweb (comprehensive R- and bioconductor-based web service for microarray data analysis) Graz (Austria)
- CellMontage (similar expression profile search server) Tokyo (Japan)
- CIMMiner (generates color-coded Clustered Image Maps (CIMs) ("heat maps") to represent "high-dimensional" data sets such as gene expression profiles) NCI (USA)
- CONFAC (application of comparative genomic promoter analysis to DNA microarray datasets) Atlanta (USA)
- CTWC Server (coupled two-way clustering analysis of breast cancer and colon cancer gene expression data) Weizmann (Israel)
- eXPatGen (Gene Expression Pattern Generator) Newark (USA)
- Express Yourself Yale (USA)
- Expression Profiler (online platform for analysis of microarray data) EBI (UK)
- FatiGO + (a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments) Valencia (Spain)
- GAP (Genome- wide Automated Primer) UCI (USA)
- GEMS (for biclustering analysis of expression data) Boston (USA)
- GeneCruiser (service for the annotation of microarray data) MIT (USA)
- GenePublisher CBS (Denmark)
- GEPAS (pipeline for microarray gene expression data) Madrid (Spain), another link
- GEPS (the Gene Expression Pattern Scanner) Fujian (China)
- GOAL (automated Gene Ontology analysis of expression profiles) Ferrara (Italy)
- INCLUSive (suite of web-based tools and is aimed at the automatic multistep analysis of microarray data) Sista (Belgium)
- ISACGH (analysis of Array CGH and gene expression) Valencia (Spain)
- JProGO (tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information) Braunschweig (Germany)
- KAAS (an automatic genome annotation and pathway reconstruction server) Kyoto (Japan)
- KARMA (application for comparing and annotating heterogeneous microarray platforms) Yale (USA)
- MADAP (a flexible clustering tool for the interpretation of one-dimensional genome annotation data) ISREC (Switzerland)
- MADTools (analysis and storage data) Nantes (French)
- MapMan (application to legume genome arrays) Canberra (Australia)
- MDscan (Fast Computational Method for Finding Protein-DNA Interaction) Stanford (USA)
- Microarray data analysis Toulouse (French)
- Microarray gene expression data analysis tools EBI (UK)
- Microarray Elements Search and Download TAIR (USA)
- MIDAW (statistical analysis of microarray data) Padua (Italy)
- Oligodb (interactive design of oligo DNA for transcription profiling of human genes) Berlin (Germany)
- OligoWiz 2.0 (integrating sequence feature annotation into the design of microarray probes) Lyngby (Denmark)
- PAP (a comprehensive workbench for mammalian transcriptional regulatory sequence analysis) Washington (USA)
- PathExpress (a web-based tool to identify relevant pathways in gene expression data) Canberra (Australia)
- Pathway Miner (extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data) Arizona (USA)
- Prism (tool for exploring sets of genome-wide data such as the data produced by expression microarrays) Washington (USA)
- ProbeLynx (tool for updating the association of microarray probes to genes) Vancouver (Canada)
- ProbeWiz Server CBS (Denmark)
- ProDesign (a fast and flexible approach to oligonucleotide probe design for genomes and gene families) Toronto (Canada)
- Prophet (class prediction using microarray data) Valencia (Spain)
- RACE (analysis computation for gene expression data) Lausanne (Switzerland)
- ROSO (optimizing oligonucleotide probes for microarrays) PBIL (French)
- SNOMAD (Standardization and NOrmalization of MicroArray Data) John Hopkins (USA)
- SOTA (DNA-array data analysis) Madrid (Spain)
- SVM (supervised cluster analysis for microarray data based on multivariate Gaussian mixture) California (USA)
- VAMPIRE microarray suite (platform for the interpretation of gene expression data) California (USA)
- VARAN (tool for analyzing variability amongst DNA microarrays experiments) ESPCI (French)
- Motifs
- CENSOR (query sequences aligned against a reference collection of human or rodent repeats) GIRI (USA)
- CDART (protein homology by domain architecture) NCBI (USA)
- Consensus (identification of consensus patterns in unaligned DNA and protein sequences) Pasteur (French)
- CREDO (tool for computational detection of conserved sequence motifs in noncoding sequences) MIPS (Germany)
- Emotif (find motifs in aligned sequences) Stanford (USA), see also 3motif
- FUZZNUC (nucleic acid pattern search) Pasteur (French)
- Gibbs Centroid Sampler (for locating conserved elements in biopolymer sequences) Providence (USA)
- IWoCS (analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships) Alicante (Spain)
- MEME (tool for discovering motifs in groups of sequences) San Diego, another link, see also Pasteur
- Pattern Scanning with Profiles Max-Planck (Germany)
- Pattern_Search (searching potential composite elements similar to the COMPEL collection) GBF (Russia)
- Probe, sequence match RDP Michigan (USA)
- Scan_for_matches Pasteur (French)
- SCOPE (for practical de novo motif discovery) Hanover (USA)
- SeSiMCMC (a Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length) Moscow (Russia)
- SMILE (tool that infers motifs in a set of sequences) à Pasteur : simple motif, with 2 boxes
- STAMP (for exploring DNA-binding motif similarities) Pittsburgh (USA)
- TRANSPO (Searching for Transposons with known TIR) LSI (Spain)
- UTRScan Bari (Italy)
- WORDMATCH (finds all exact matches of a given size between 2 DNA sequences) Pasteur (French)
- PCR primer selection
- Tools at Weizmann (Israel)
- Aide PCR (in french) U-Descartes (French)
- AcePrimer (automation of PCR primer design based on gene structure) Vancouver (Canada)
- AMOD (a morpholino oligonucleotide selection tool) Minnesota (USA)
- AOPredict (Antisense Oligonucleotide Prediction Program) Karolinska (Sweden)
- ASePCR (alternative splicing electronic RT-PCR in multiple tissues and organs) Seoul (Korea)
- Assembly PCR oligo maker (a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production) Toronto (Canada)
- BayesMiRNAfind (combining multi-species genomic data for microRNA identification using a Naïve Bayes classifier) Philadelphia (USA)
- BiSearch (primer-design and search tool for PCR on bisulfite-treated genomes) Budapest (Hungary)
- Cascade (16S rDNA prokaryotic multiple sequence alignment (prokMSA) for browsing, blasting, probing) LLNL (USA)
- CloneIt (finding cloning strategies, in-frame deletions and frameshifts) INRA (French)
- CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primers) Blocks (USA)
- DAN (calculates DNA RNA/DNA melting temperature) Pasteur (French)
- DEQOR (tool for the design and quality control of siRNAs) Max Planck (Germany)
- DoPrimer (Germany)
- DyNAVacS (an integrative tool for optimized DNA vaccine design) Delhi (India)
- Electronic PCR (PCR-based sequence tagged sites (STSs)) NCBI (USA)
- E-RNAi (to design optimized RNAi constructs) Heidelberg (Germany)
- ExPrimer (to design primers from exon-exon junctions) Bangalore (India)
- FractTM (a fractional programming approach to efficient DNA melting temperature calculation) Koln (Germany)
- Gene2Oligo (oligonucleotide design for in vitro gene synthesis) Michigan (USA)
- GeneFisher Bielefeld (Germany)
- G-PRIMER (greedy algorithm for selecting minimal primer set) Singapore
- Hyther WSU (USA)
- ISOCHORE (plots isochores in large DNA sequences) Pasteur (French)
- MEDUSA Karolinska (Sweden)
- MELTING (enthalpie, entropy and melting temperature) Pasteur (French)
- MethPrimer (Design Primers for Methylation PCRs) UCSF (USA)
- mPrimer3 (enhancements and modifications of primer design program Primer3) Tartu (Estonia)
- MuPlex (multi-objective multiplex PCR assay design) Boston (USA)
- MutScreener (primer design tool for PCR-direct sequencing) Chicago (USA)
- NTMG (N-terminal Truncated Mutants Generator for cDNA : an automatic multiplex PCR assays design for generating various N-terminal truncated cDNA mutants) Taichung (Taiwan)
- Oligo Calc Chicago (USA)
- Oligo Calculator (Java script) Pittsburg (USA)
- Oligo Calculator BioInf (USA)
- Oligodb (interactive design of oligo DNA for transcription profiling of human genes) Berlin (Germany)
- OligoFAktory (a visual tool for interactive oligonucleotide design) Brussells (Belgium)
- PCR designer for restriction analysis of various types of sequence mutation Oxford (UK)
- PCR Suite (Overlapping_Primers, Genomic_Primers, SNP_Primers, cDNA_Primers) Rotterdam (The Netherlands)
- PhylArray (phylogenetic probe design algorithm for microarray) Clermont-Ferrand (French)
- PIRA (PCR designer for restriction analysis of single nucleotide polymorphisms) Southampton (UK)
- PRIDE (PRImer DEsign for large scale sequencing) TBI (Germany)
- PriFi (using a multiple alignment of related sequences to find primers for amplification of homologs) Aarhus (Denmark)
- PRIMA (selects primers for PCR and DNA amplification) Pasteur (French)
- Primaclade (a flexible tool to find conserved PCR primers across multiple species) Saint Louis (USA)
- Primegens (PRIMEr Design Using GEN Specific Fragments) ORNL (USA)
- Primer 3 MIT (USA), see also UMMS (USA)
- Primer3Plus Wageningen>/A> (The Netherlands)
- The Primer Generator Johns Hopkins (USA)
- PrimerStation (a highly specific multiplex genomic PCR primer design server for the human genome) Tokyo (Japan)
- PrimerZ (streamlined primer design for promoters, exons and human SNPs) Taipei (Taiwan)
- Primo (Prediction of forward and reverse oligonucleotide Primers) Pasteur (French)
- Primo MSP (methylation specific PCR Primer design) Chang Bioscience
- QPRIMER (for designing conserved PCR primers from multigenome alignments) UCLA (USA)
- Radiation Hybrid Mapping MIT (USA)
- RAGPOOLS (RNA-As-Graph-Pools-a tool for assisting the design of structured RNA pools for in vitro selection) New York (USA)
- SIDE (siRNA design, highly specific and accurate selection of siRNAs for high-throughput functional assays) Madrid (Spain)
- siDirect (target-specific siRNA design software for mammalian RNA interference) Tokyo (Japan)
- siRNA selector Philadelphia (USA)
- siRNA Design Tool (filtering, ...) Hong Kong (UK)
- siVirus (antiviral siRNA design software for highly divergent viral sequences) Tokyo (Japan)
- SNPbox (primer design from gene to genome) Antwerp (Belgium)
- SNP Cutter (a comprehensive tool for SNP PCR-RFLP assay design) Chicago (USA)
- SOP3v2 (selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms) Pittsburgh (USA)
- SSRPrimer and SSR Taxonomy Tree (Biome SSR discovery) Victoria (Australia)
- SSR primer (simple sequence repeat marker loci discovery) Victoria (Australia)
- STSSEARCH (searches a DNA database for matches with a set of STS primers) Pasteur (French)
- TROD (short interfering RNAs (siRNAs) with T7 RNA polymerase) Genève (Switzerland)
- VecScreen (tool for screening a nucleotide sequence for vector) NCBI (USA)
- Virtual PCR Brno (Czech Republic)
- vPCR Padua (Italy)
- WatCut (Cleave your DNA online, and create new cleavage sites in your oligos using silent mutations) Waterloo (Canada)
- WCLUSTAG (combining functional and linkage disequilibrium information in the selection of tag SNPs) Hong Kong
- Web Primer (Saccharomyces) Stanford
- Bellerophon (detects chimeric sequences in multiple sequence alignments 16S rDNA) Brisbane (Australia)
- Chimera detection (Detection of chimeric 16S rRNA artifacts generated by PCR amplification) USC (USA)
- Prediction of gene structure (exons, splicing sites, promotors...)
- AAT (Analysis and Annotation Tool for Finding Genes in Genomic Sequences) Michigan (USA)
- ACTG (Automatic correspondence of tags and genes : a tool for the analysis of SAGE, MPSS and SBS data) Harvard (USA)
- AGenDA (gene-prediction tool that is based on cross-species sequence comparison) Bielefeld (Germany)
- ASGS (an alternative splicing graph web service) Singapore
- Ann-spec (locates common DNA regulatory patterns in a set of promoter region sequences) CBS (Denmark)
- ARFA (for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting) Utah (USA)
- ARGO (detection of degenerate motifs and large-scale recognition of eukaryotic promoters) Novosibirsk (Russian)
- ASmodeler (gene modeling of alternative splicing events) Seoul (Korea)
- ASPIC (alternative splicing prediction and transcript isoforms characterization) Bari (Italy)
- AUGUSTUS (ab initio prediction of alternative transcripts) Gottingen (Germany)
- Bacterial Promoter, Operon and Gene Finding SoftBerry
- BASys (automated bacterial genome annotation) Alberta (Canada)
- BioProspector (Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes) Stanford (USA)
- BIPASS (bioInformatics pipeline alternative splicing services) Arizona (USA)
- BLISS 2.0 (tool for predicting conserved regulatory modules in distantly-related orthologous sequences) Gainesville (USA)
- Gene Find (exons, splicing sites, promoter, coding region) SoftBerry
- Gene Feature Searches BCM (USA)
- Cassandra (Recognition of protein-coding segments in eukaryotic DNA) USC (USA)
- CDS (Search Coding Regions) Pasteur, see also advanced form (French)
- CHECKTRANS (ORF property statistics) Pasteur (French)
- CisMols Analyzer (identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes) Cincinnati (USA)
- Cister (Cis-element Cluster Finder) Boston (USA)
- Cister (Cis-element Cluster Finder) Boston (USA)
- ClusterDraw (tool to identify and visualize clusters of binding motifs for transcription factors) Berkeley (USA)
- CMA (a fitness-based tool for identification of transcription factor binding site combinations) Wolfenbuttel (Germany)
- CONREAL (identification and visualization of conserved transcription factor binding sites) Utrecht (The Netherlands)
- ConSite (prediction of regulatory elements using cross-species comparison) Stockholm (Sweden)
- Correspondence Analysis Lyon (French)
- CPC (assess the protein-coding potential of transcripts using sequence features and support vector machine) Beijing (China)
- CpGProD (CpG Island Promoter Detection) PBIL (French)
- DIANA-EST (for predicting coding regions in EST sequences) Pennsylvania (USA)
- DIANA-TIS (for predicting coding starts in EST sequences) Pennsylvania (USA)
- DIANA-MicroT (or the prediction of microRNA targets) Pennsylvania (USA)
- Diogenes (examines short genomic sequences for the presence of likely protein-encoding regions) UMN (USA)
- DoubleScan (for comparative ab initio prediction of protein coding genes in mouse and human DNA) Sanger (UK)
- dPattern (transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis) Indiana (USA)
- Dragon Genome Explorer (Promoter finder, CG+ PF, ATG finder, CpGIslands, Splice sites, PolyA) BRUS (Singapore)
- Dragon Promoter Mapper (Bayesian framework for modelling promoter structures) BRUS (Singapore)
- E2F transcription factor binding DNA-site EMBNet (Russia)
- Eponine (mammalian transcription start sites) Sanger (UK)
- ESTExplorer (an expressed sequence tag (EST) assembly and annotation platform) Singapore
- ESTpass (for processing and annotating expressed sequence tag (EST) sequences) Daejeon (Korea)
- EasyGene 1.2 (produces a list of predicted genes for a chosen prokaryotic genome) Copenhagen (Denmark), see also Easy Gene 1
- Eukaryotic Promoter Prediction by Neural Network Berkeley (USA)
- FirstEF (first-exon and promoter prediction program for human DNA) UCSC (USA), see also CSHL (USA)
- FOOTER (finds mammalian DNA regulatory regions using phylogenetic footprinting) Pittsburgh (USA)
- FootPrinter3 (phylogenetic footprinting in partially alignable sequences) Montreal (Canada)
- FrameD (genes and frameshifts in procaryotic sequences) INRA (French)
- FramePlot NIH-NET (Japan)
- FrameShift Error Detection EMBL, see also ERR_WISE (Germany)
- FTG prediction (Genescan, Lengthen-shuffle, FTG) Chandigarh (India)
- FunSiteP (recognition and classification of eukaryotic promoters by searching transcription factor binding sites) GRESA (Russia)
- GeneAlign (a coding exon prediction tool based on phylogenetical comparisons) Hsinchu (Taiwan)
- GeneComber (combining outputs of gene prediction programs for improved results) Vancouver (Canada)
- GeneFizz (tool for the comparision between genetic (coding/non-coding) and physics (helix/coil) segmentations of DNA sequences) Pasteur (French)
- Gene Finder (Human, Mouse, Arabidopsis, Fission Yeast) CSHL (USA)
- Gene finding (Human, Drosophila, Nematode, Yeast, Plant) London (UK)
- Gene Finding in Viral Genomes SoftBerry
- GeneMark EBI (UK)
- GeneMark (gene finding in prokaryotes, eukaryotes and viruses) Atlanta (USA)
- Generation (microbial gene prediction) ORNL (USA)
- Gene Recognition via Spliced Alignment USC (USA)
- Geneid IMIM
- GeneSplicer TIGR (USA)
- Genie (gene finder based on Hidden Markov Models) Berkeley (USA)
- GenomeScan (predicting the locations and exon-intron structures of genes) MIT (USA)
- GenoMiner (a tool for genome-wide search of coding and non-coding conserved sequence tags) Milan (Italy)
- GeneSeqer (identifies potential exon/intron structure in pre-mRNA) ZmDB (USA), see also for plants AtGDB
- GETORF (finds and extracts open reading frames) Pasteur (French)
- GenScan (Identification of complete gene structures in genomic DNA) Pasteur (French), see also GeniusNet (Germany), see also MIT (USA), see also Harvard
- GRAIL ORNL, another link Oak Ridge (Exons, repeats, Poly A sites, CpG)
- HMMgene (Prediction of genes in vertebrate and C. elegans) CBS (Denmark)
- Human Core-Promoter Finder CSHL (USA)
- IsoFinder (computational prediction of isochores in genome sequences) Granada (Spain)
- jPREdictor (tool for the prediction of cis-regulatory elements) Bielefeld (Germany)
- Match (for searching potential binding sites for transcription factors) GBF (Russia)
- MatCompare (similarity of position frequency matrices for transcription factor binding sites) CSHL (USA)
- MELINA (motif extraction from promoter regions of potentially co-regulated genes) Tokyo (Japan)
- MICheck (tool for fast checking of syntactic annotations of bacterial genomes) Evry (French)
- Microbial gene prediction ORNL (USA)
- MicroFootPrinter (a tool for phylogenetic footprinting in prokaryotic genomes) Washington (USA)
- MoD Tools (regulatory motif discovery in nucleotide sequences from co-regulated or homologous genes) Milano (Italy)
- Motif-Search (comparative analysis of methods for representing and searching for transcription factor binding sites) Princeton (USA)
- MotifViz (an analysis and visualization tool for motif discovery : three motif discovery programs, Clover, Rover and Motifish) Boston (USA)
- mRNA ORF finder WUSTL (USA)
- MSCAN (identification of functional clusters of transcription factor binding sites) Stockholm (Sweden)
- NAST (a multiple sequence alignment server for comparative analysis of 16S rRNA genes) Berkeley (USA)
- NetGene2 CBS (Denmark)
- NetPlantGene V2.0 (neural network predictions of splice site prediction in Arabidopsis thaliana DNA) CBS (Denmark)
- NetStart (predictions of translation start in vertebrate and Arabidopsis) CBS (Denmark)
- NetUTR (plice sites in 5' UTR regions of human genes) CBS (Denmark)
- Nucleotide Sequence Analysis (Splice sites, Protein coding (Human, Drosophila, C. Elegans, Yeast, Plant, E. Coli) and Gene model construction, Promotor and poly-A regions recognition, BestORF, FGenes...) SoftBerry
- NXSensor (for evaluating DNA for nucleosome exclusion sequences and accessibility to binding factors) Burnaby (Canada)
- oPOSSUM (integrated tools for analysis of regulatory motif over-representation) Vancouver (Canada)
- ORF Finder (graphical analysis tool) NCBI (USA)
- OrfPredictor (predicting protein-coding regions in EST-derived sequences) Montreal (Canada)
- OSCAR (one-class SVM for accurate recognition of cis-elements) Beijing (China)
- PEAKS (identification of regulatory motifs by their position in DNA sequences) Barcelona (Spain)
- PLACE Signal Scan (Plant Cis-acting Regulatory DNA Elements) DISC (Japan)
- PLOTORF (plot potential open reading frames) Pasteur (French)
- Plot ORFs UMMS (USA)
- POBO (transcription factor binding site verification with bootstrapping) Helsinki (Finland)
- POCO (discovery of regulatory patterns from promoters of oppositely expressed gene sets) Helsinki (Finland)
- PolyA signals CSHL (USA)
- Position dependencies in transcription factor binding sites Basel (Switzerland)
- POXO (tool series to discover transcription factor binding sites) Helsinki (Finland)
- PredictRegulon (prediction of the regulatory protein binding sites and operons in prokaryote genomes) EMBnet (India)
- PromAn (an integrated knowledge-based server dedicated to promoter analysis) Strasbourg (French)
- PROMO (identification of putative transcription factor binding sites) LSI (Spain)
- PromScan (scan DNA sequences for potential sigma54-RNAP-binding sites) Ontario (Canada)
- Prokaryotic promoter analysis using SAK London (UK)
- Promoter classification EMBNet (Russia)
- Promoter 2 (vertebrate Pol II promoters) CBS (Denmark)
- ProMiR II (probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs) Seoul (Korea)
- Proscan II (predicts putative eukaryotic Pol II promoter sequences) NIH (USA)
- Putative DNA Sequencing Errors Check EMBL-Bork (Germany)
- Recon (Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis) MBS (Russia)
- Regulatory Sequence Analysis Tools UCMB-ULB (Belgium)
- RegRNA (for identifying regulatory RNA motifs and elements) Hsin-Chu (Taiwan)
- RESCUE-ESE (identifies candidate exonic splicing enhancers in vertebrate exons) MIT (USA)
- RecSta (coding region (CDS or exon) prediction program using COA) Lyon (French)
- RibEx (locates riboswitches and other conserved bacterial regulatory elements) Mexico (Mexico)
- RiceHMM (Gene Prediction Program for Rice) RGP (Japan)
- RNAhybrid (microRNA target prediction easy, fast and flexible) Bielefeld (Germany)
- Search Genes and Coding Regions (CDS, Xpound, Genescan, Genemark, GRAIL, MORGAN, GLIMMER) Pasteur (French)
- SAGExplore (for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation) Santagio (Chile)
- Sequence Quality Check (given a sequence or a list of sequences in FASTA format, this tool predicts they represent real genes) Texas (USA)
- ShiftDetector (detection of shift mutations) Volcani (Israel)
- Shops (show operon structures) Utrecht (The Netherlands)
- SITECON (tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition) Novosibirsk (Russia)
- SNP discovery Victoria (Australia)
- SNPmasker (automatic masking of SNPs and repeats across eukaryotic genomes) Tartu (Estonia)
- SNPsFinder (application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes) LANL (USA)
- SNP (predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information) Bologna (Italy)
- ssSNPer (identifying statistically similar SNPs to aid interpretation of genetic association studies) Queensland (Australia)
- SPADS (Specific Primer and Amplicon Design Software) Genoplante (French)
- SpliceMachine (predicting splice sites from high-dimensional local context representations) Gent (Belgium)
- SplicePort (interactive splice-site analysis tool) Maryland (USA)
- SplicePredictor (identifies potential splice sites in (plant) pre-mRNA) ZmDB (USA)
- Splice Site Prediction by Neural Network Berkeley (USA)
- STRING (Search Tool for Recurring Instances of Neighbouring Genes) EMBL (Germany)
- Stubb (a program for discovery and analysis of cis-regulatory modules) Rockefeller (USA)
- Suite of web-based programs to search for transcriptional regulatory motifs (BioProspector, CompareProspector, MDscan) Stanford (USA)
- SynoR (identifying synonymous regulatory elements in vertebrate genomes) Livermore (USA)
- TACT (Transcriptome Auto-annotation Conducting Tool of H-InvDB) Tokyo (Japan)
- TAP (Transcript Assembly Program) and TIP (Transcript Isoform Prediction) WUSTL (USA)
- TargetIdentifier (for identifying full-length cDNAs from EST sequences) Montreal (Canada)
- TESS (Transcription Element Search System) CBIL (USA)
- TFBIND (searching transcription factor binding sites) RIKEN (Japan)
- TFBScluster (identification of mammalian composite regulatory elements) Cambridge (UK)
- TFBS (Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes) Braunschweig (Germany)
- TFExplorer (integrated analysis database for predicted transcription regulatory elements) Daejeon (Korea)
- TFM-Explorer (analysis of regulatory regions in Human and Mouse genomes) Lille (French)
- TFSCAN (scans DNA sequences for transcription factors) Pasteur (French)
- TICO (a tool for improving predictions of prokaryotic translation initiation) Gottingen (Germany)
- T-Reg Comparator (analysis tool for the comparison of position weight matrices) Max Planck (Germany)
- TRES (Comparative Promoter Analysis) Singapore
- tRNA and tmRNA detection (Aragorn, Arwen, Bruce) Rydeback (Sweden)
- tRNAscan (Search for transfer RNA genes in genomic sequence) Washington (USA), see also Pasteur, see also FAStRNA Pasteur (French)
- tRNAscan-SE, snoscan and snoGPS (for the detection of tRNAs and snoRNAs) California (USA)
- VOMBAT (prediction of transcription factor binding sites using variable order Bayesian trees) Gatersleben (Germany)
- WordSpy (identifying transcription factor binding motifs by building a dictionary and learning a grammar) Saint Louis (USA)
- WWW AntiHunter (tool to detect potential EST antisense transcripts) Milan (Italy), see also AntiHunter 2.0
- Xpound Pasteur, see also advanced form (French)
- Profile of thermal denaturation
- dnaMATE (a consensus melting temperature prediction server for short DNA sequences) Santiago (Chile)
- DINAMelt (nucleic acid melting prediction) RPI (USA)
- MELTING (enthalpie, entropy and melting temperature) Pasteur (French)
- Poland Dusseldorf (Germany)
- Oligo Tm Berkeley (USA)
- Oligo Tm genelink
- Stitchprofiles.uio.no (analysis of partly melted DNA conformations using stitch profiles) Oslo (Norway)
- Repeats
- ACMES (fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval) Missouri (USA)
- CRISPRFinder (to identify clustered regularly interspaced short palindromic repeats) Orsay (French)
- DomainOrganizer (organization within repeated DNA sequences: application to the study of a family of transposable elements) Rennes (French)
- Dot Plot Duesseldorf (Germany)
- EINVERTED (finds DNA inverted repeats) Pasteur (France)
- EQUICKTANDEM (finds tandem repeats) Pasteur (France)
- ETANDEM (looks for tandem repeats in a nucleotide sequence) Pasteur (France)
- IMEx (Imperfect Microsatellite Extractor) Hyderabad (India)
- MREPATT (Consecutive Multiple REpeated PATTerns) LSI (Spain)
- MREPS (finding tandem repeats) LIFL (French)
- PALINDROME (looks for inverted repeats in a nucleotide sequence) Pasteur (French)
- PLOTREP (defragmentation and visual analysis of dispersed genomic repeats) Godollo (Hungary)
- RepeatFinder Cornell (USA)
- RepeatMasker (screens DNA sequences against a library of repetitive elements) Washington (USA)
- RepeatMasker (screens DNA sequences for low complexity DNA sequences and interspersed repeats) EMBL (Germany)
- Repeats Pasteur (France)
- RepFind ZLab (USA)
- REPuter (computes all maximal duplications and reverse, complemented and reverse complemented repeats in a DNA sequence) Bielefeld (Germany)
- Satellites (identifying satellites and periodic repetitions) Pasteur (France)
- SIMPLE UCL (UK)
- Spectral Repeat Finder (Fourier transformation) Chandigarh (India)
- Sputnik (DNA microsatellite repeat search utility) Bordeaux (French)
- STAR (an algorithm to search for Tandem Approximate Repeat) Montpellier (French)
- Tandem repeats New York (USA)
- Tandem repeats finder Boston (USA)
- Specific sites search
- bSECISearch (a search and prediction program for bacterial SECIS elements) Nebraska (USA)
- COMET (significant clusters of motifs in a DNA sequence) ZLab (USA)
- ConSite (prediction of regulatory elements using cross-species comparison) Stockholm (Sweden)
- CRSD (composite regulatory signature discovery) Taipei (Taiwan)
- dsCheck (highly sensitive off-target search software for double-stranded RNA-mediated RNA interference) Tokyo (Japan)
- DP-Bind (sequence-based prediction of DNA-binding residues in DNA-binding proteins) Albany (USA)
- ELM (predicting functional sites (described by linear motifs) in eukaryotic proteins) EMBL (Germany)
- GeMprospector (design of cross-species genetic marker candidates in legumes and grasses collection of ESTs) Aarhus (Denmark)
- Improbizer (motifs in DNA or RNA sequences that occur with improbable frequency) UCSC (USA)
- LTR_FINDER (an efficient tool for the prediction of full-length LTR retrotransposons) Shanghai (China)
- MethCGI (predicting methylation status of CpG islands in the human brain) Tsinghua (China)
- microHARVESTER (identification of plant microRNA homologs) Tubingen (Germany)
- MicroInspector (detection of miRNA binding sites in an RNA sequence) Heraklion (Greece)
- MilPat (searching RNA motifs and their intermolecular contacts with constraint networks) Toulouse (French)
- MiPred (classification of real and pseudo microRNA precursors using random forest prediction model with combined features) Nanjing (China)
- MirAlign (MicroRNA identification based on sequence and structure alignment) Beijing (China)
- miRU (plant miRNA target prediction) Ardmore (USA)
- Motif Sampler (find over-represented motifs in the upstream region of a set of co-regulated genes) Leuven (Belgium)
- MSCAN (identification of functional clusters of transcription factor binding sites) Stockholm (Sweden)
- NetStart (predictions of translation start in vertebrate and Arabidopsis) CBS (Denmark)
- PolyA signals CSHL (USA)
- PupaSuite (finding functional single nucleotide polymorphisms for large-scale genotyping purposes) Valencia (Spain)
- Predicting activities of functional sites in DNA/RNA MBS (Russia)
- Primary microRNA prediction and processing Trondheim (Norway)
- ProMiR II (probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs) Seoul (Korea)
- PROMO (identification of putative transcription factor binding sites) LSI (Spain)
- RGSiteScan program (potential binding sites of 37 transcription factors) MBS (Russia)
- RTAnalyzer (for finding new retrotransposons and detecting L1 retrotransposition signatures) Sherbrooke (Canada)
- S_Site (searching for E2F sites) GBF (Russia)
- siDirect (target-specific siRNA design software for mammalian RNA interference) Tokyo (Japan)
- siRNA selector Philadelphia (USA)
- SITECON (tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition) Novosibirsk (Russia)
- Suite of web-based programs to search for transcriptional regulatory motifs (BioProspector, CompareProspector, MDscan) Stanford (USA)
- TFSEARCH : Searching Transcription Factor Binding Sites (Japan), another link
- TFScan (locates potential transcription factor binding sites) UMMS (USA)
- TESS (Transcription Element Search System) CBIL (USA)
- TICO (a tool for postprocessing the predictions of prokaryotic translation initiation sites) Gottingen (Germany)
- Zinc Finger Tools (custom DNA-binding domains for transcription factors and nucleases) California (USA), autre lien
- Structure
- AMSAG (energy landscape of k-point mutants of an RNA molecule) Boston (USA)
- ARTS (for aligning RNA tertiary structures) Tel Aviv (Israel)
- Bend.it (Prediction of bendability and propensity to curvature from DNA sequences) ICGEB (Italy)
- CARNAC (folding families of related RNAs) Lille (French)
- CMfinder (a covariance model based RNA motif finding algorithm) Washington (USA)
- CONTRAfold (RNA secondary structure prediction without physics-based models) Stanford (USA)
- CRAFT (DNA Bending Stiffness Features) MBS (Russia)
- DNA RNA Folding (Zuker) RPI, mirror at MBC (Australia), mirror at Bielefeld (Germany)
- ERPIN (tool to profile-based RNA motif identification) Marseille (French)
- GPRM (finding common secondary structure elements) Chiao Tung (Taiwan)
- GUUGle (A utility for fast exact matching under RNA base pairing rules) Bielefeld (Germany)
- HPknotter (an heuristic approach for detecting RNA H-type pseudoknots) Taiwan (China)
- ILM (predicting RNA secondary structures with pseudoknots) Washington (USA)
- Kinefold (RNA/DNA folding path and structure prediction including pseudoknots and knots) Institut Curie (French)
- INFO-RNA (for fast inverse RNA folding satisfying sequence constraints) Freiburg (Germany)
- Model.it (3D model of DNA molecule) ICGEB (Italy)
- MIGAL (a tool for RNA secondary structure comparison) Marne la Vallée (French)
- paRNAss (Prediction of Alternative RNA Secondary Structures) Bielefeld (Germany)
- Pfold (takes an alignment of RNA sequences as input and predicts a common structure) Aarhus (Denmark)
- Plot.it (Plotting of general DNA parameters) ICGEB (Italy)
- PMmatch (alignment of structural RNAs) Vienna (Austria)
- PseudoViewer (for visualizing RNA pseudoknots and secondary structures) Inchon (Korea)
- QGRS Mapper (for predicting G-quadruplexes in nucleotide sequences) New Jersey (USA)
- Quadfinder (identification and analysis of quadruplex-forming motifs in nucleotide sequences) Delhi (India)
- Quikfold (Fold many short RNA or DNA sequences at once) RPI (USA)
- RDfolder (prediction of RNA secondary structure) Beijing (China)
- Riboswitch finder (a tool for identification of riboswitch RNAs) Wurzburg (Germany)
- RNA Analysis (Mfold, RNAfold, eval, heat..) Pasteur (France)
- RNA Analyzer Wuerzburg (Germany)
- RNAbor (Boltzmann probability of RNA structural neighbors and riboswitch detection) Uppsala (Sweden)
- RNA & DNA Folding (Zuker) RPI (USA)
- RNA secondary structure prediction Moscou
- RNAfold Vienna (Austria)
- RNAGA (prediction of common secondary structures of RNAs by genetic algorithm) Pasteur (French)
- RNALOSS (for RNA locally optimal secondary structure computation) Boston (USA)
- RNA Movies 2 (sequential animation of RNA secondary structures) Bielefeld (Germany)
- RNAMST (efficient and flexible approach for identifying RNA structural homologs) Hsin-Chu (Taiwan)
- RNASoft (PairFold, CombFold, RNA Designer) Columbia (Canada)
- RNAz (prediction of thermodynamically stable and evolutionarily conserved RNA structures) Vienna (Austria)
- SCARNA (fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments) Chiba (Japan)
- Sfold (Sirna, Soligo, Sribo, Srna) New York (USA), another link
- SSU (rRNA Secondary Structure Prediction and Alignment) UCSC (USA)
- SwS (a solvation service for nucleic acids) Strasbourg (French)
- taveRNA (a web suite for RNA algorithms and applications) Washington (USA)
- Tinoco Plot Duesseldorf (Germany)
- WebSIDD (predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA) California (USA)
- WEBTHERMODYN (stability profile of a DNA duplex) Buffalo (USA)
- Zipfold (Compute minimum folding energies only for many RNA or DNA sequences) RPI (USA)
- Translation
- ATID (alternative translational initiation database) Beijing (China)
- COMBAT (comparison of coding DNA) Pasteur (France)
- EMBOSS at Pasteur (France)
- Translate nucleic acid sequences TRANSEQ, see also UMMS
- Back translate a protein sequence BACKTRANSEQ
- Output sequence with translated ranges PRETTYSEQ
- Pretty output of DNA translations SHOWORF
- Colorado Translate, voir aussi Reverse Translate (USA)
- Expasy (Switzerland)
- NIH
- TICO (a tool for postprocessing the predictions of prokaryotic translation initiation sites) Gottingen (Germany)
- Virtual Ribosome (a comprehensive DNA translation tool with support for integration of sequence feature annotation) CBS (Denmark)
- BLOCKS
- BLIMPS (BLocks IMProved Searcher) Pasteur (France)
- BLOCKS WWW Server FHCCRC (search and construction) (Hutchinson)
- IMPALA (Search BLOCKS) FHCRC (USA)
- Identification of protein family
- Cascade (homology search tool for relating protein domains) Bangalore (India)
- Cognitor (Compare your sequence to COG database) NCBI (USA)
- CysView (protein classification based on cysteine pairing patterns) Terrace (Singapore)
- DiffTool (building, visualizing and querying protein clusters) Pasteur (French)
- EMatrix Stanford (USA), another link link
- Family Pairwise Search SDSC (USA)
- FAN (fingerprint analysis of nucleotide sequences) Manchester (UK)
- FISH (family identification of sequence homologues using structure anchored hidden Markov models) Umea (Sweden)
- GIST-SVM (mismatch string kernels for discriminative protein classification) Columbia (USA)
- HHsenser (exhaustive transitive profile search using HMM-HMM comparison) Tubingen (Germany)
- HoSeqI (automated homologous sequence identification in gene family databases) PBIL (French)
- Identify (from the BLOCKS and PRINTS databases) Stanford (USA)
- iMOT (for identifying conserved spatially interacting regions across proteins) Uttar Pradesh (India)
- MAGIIC-PRO (detecting functional signatures by efficient discovery of long patterns in protein sequences) Taipei (Taiwan)
- MitoPred (a genome-scale method for predicting mitochondrial proteins) Albany (USA)
- MOTIF (Prosite, Blocks, Prodom, Prints, Pfam) Kyoto (Japan)
- PDART (an initial strategy for comparing proteins at the domain architecture level) Beijing (China)
- PeCoP (automatic determination of persistently conserved positions in protein families) Bioinformatics (USA)
- Picasso (generating a covering set of protein family profiles) EMBL-EBI (UK)
- PLEX (protein function prediction using the Protein Link EXplorer) Texas (USA)
- PP1 (identify putative Protein Phosphatase 1 (PP1) binding proteins) Pasteur (French)
- FingerPRINTScan EBI (UK)
- ProTarget (Selecting targets for structural determination by navigating in a graph of protein families) Jerusalem (Israel)
- ProTeus (identification of short linear signatures in protein termini) Jerusalem (Israel)
- PSCAN (scans proteins using PRINTS) Pasteur (France), see also UMMS (USA)
- P-val FingerPRINTScan Manchester (UK)
- QC-COMP (comparison of profile hidden Markov models for protein families) Newark (USA)
- Search the PRINTS & PROSITE Database London (UK)
- SVMMER (classification and characterization of proteins) ANL (USA)
- WebProAnalyst (analysis of quantitative structure-activity relationships in protein families) Novosibirsk (Russian)
- Motifs
- Cascade (homology search tool for relating protein domains) Bangalore (India)
- Consensus (identification of consensus patterns in unaligned DNA and protein sequences) Pasteur (France)
- DOMAC (an accurate, hybrid protein domain prediction server) Florida (USA)
- DOUTfinder (identification of distant domain outliers using subsignificant sequence similarity) Vienna (Austria)
- Emotif (find motifs in aligned sequences) Stanford (USA)
- FUZZPRO (protein pattern search) Pasteur (France)
- GPCR Subfamily Classifier UCSC (USA)
- GPCRpred (an SVM-based method for prediction of families and subfamilies of G-protein coupled receptors) Chandigarh (India)
- GPCRsclass (tool for the classification of amine type of G-protein-coupled receptors) Chandigarh (India)
- GRIFFIN (predicting GPCR-G-protein coupling selectivity using a support vector machine and a hidden Markov model) Tokyo (Japan)
- HHsenser (exhaustive transitive profile search using HMM-HMM comparison) Tubingen (Germany)
- MAGIIC-PRO (detecting functional signatures by efficient discovery of long patterns in protein sequences) Taipei (Taiwan)
- MEME (tool for discovering motifs in groups of sequences) San Diego
- PATMATMOTIFS (search a motif database with a protein sequence) Pasteur (France)
- PLSearch (search protein sequences for similarity to AACC patterns) Pasteur
- Pratt (a pattern discovery tool) Bergensis (Norway), see also EBI, see also InfoBioGen (Hong Kong), see also Expasy
- PRED-GPCR (GPCR recognition and family classification server) Athens (Greece)
- PRED-COUPLE (prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks) Athens (Greece)
- QuasiMotiFinder (identification of signatures and signature-like patterns in protein sequences) Tel Aviv (Israel)
- SCANMOT (searching for similar sequences using a simultaneous scan of multiple sequence motifs) Bangalore (India)
- Scan_for_matches Pasteur (France)
- SEARCHGTr (analysis of glycosyltransferases involved in glycosylation of secondary metabolites) New Delhi (India)
- SMART (Simple Modular Architecture Research Tool) EMBL (Germany)
- Prosite (search a sequence for a "prosite" pattern)
- Profile
- HMMBuild PBIL (French)
- MOTIF (Generate a profile from multiple sequence alignment) Kyoto (Japan)
- PFTools Pasteur (France)
- PROPHET (gapped alignment for profiles) Pasteur (France)
- Repeats
- RADAR (Rapid Automatic Detection and Alignment of Repeats in protein sequences) EBI (UK)
- Recognition of protein sequence repeats (REPRO) Amsterdam (The Netherlands)
- REP (search your protein for a collection of repeats) EMBL (Germany)
- Analysis tools package
- BCM Search Launcher BCM (USA)
- HNB (Family, function, structure) Heidelberg (Germany), see also SNAPper
- META PredictProtein server (SignalP, NetOglyc, NetPicoRNA, ChloroP, JPred, TmHMM, ToPred, DAS, FRSVR, SAMT98, Swiss-Model, CPHmodels) Columbia (USA), another link
- Network Protein Sequence @nalysis (SOPM, SOPMA, HNN, MLRC, DPM, DSC, GOR, PHD, PREDATOR,..) PBIL (French)
- PROFEAT (for computing structural and physicochemical features of proteins and peptides from amino acid sequence) Singapore
- PROSPECT-PSPP (an automatic computational pipeline for protein structure prediction) Georgia (USA)
- Analyze
- AA Composition, MW, OD, pI, titration curve ABIM (in french)
- pI et Mw Expasy
- ASAP (Analysis of Sequence and Aminoacid Probabilities) California (USA)
- ASC IMP (Analysis of protein surface : Van-der-Waals, energy, Hydrophilicity, Hydrophobicity)
- BProSite (identification of protein sites with biased amino acid properties) Albany (USA)
- ConSeq (identification of functionally and structurally important residues) Tel Aviv (Israel)
- CUTTER (generate peptide fragments by the enzymatic or chemical cleavage) Tours (France)
- Cysteines Bonding State and Connectivity Predictor Firenze (Italy), another link
- DiANNA (unified software for Cysteine state and Disulfide Bond partner prediction) Boston (USA)
- Disulfide (improving disulfide connectivity prediction with sequential distance between oxidized cysteines) Taipei (Taiwan)
- EMBOSS at Pasteur (France)
- Protein charge plot CHARGE
- Protein proteolytic enzyme or reagent cleavage digest DIGEST
- Build domain coordinate files DOMAINER
- Displays a wordmatch dotplot of two sequences DOTTUP
- Calculates Km and Vmax for an enzyme reaction FINDKM
- Hydrophobic moment calculation HMOMENT
- Displays protein hydropathy PEPWINDOW
- Displays protein hydropathy of a set of sequences PEPWINDOWALL
- Displays protein hydropathy OCTANOL
- Calculates the isoelectric point of a protein IEP
- Protein statistics PEPSTATS
- GDAP (tool for genome-wide protein disulfide bond prediction) Los Angeles (USA)
- Glycomod (predict the possible oligosaccharide structures from determined masses of a protein) Expasy (Switzerland), see also Glycanmass
- HCA (Hydrophobic Cluster Analysis) Jussieu (France)
- Hydrogen Exchange Rate Estimation FCCC (USA)
- iPTREE-STAB (interpretable decision tree based method for predicting protein stability changes upon mutations) Tokyo (Japan)
- JVirGel 2.0 (computational prediction of proteomes separated via two-dimensional gel electrophoresis under consideration of membrane and secreted proteins) Braunschweig (Germany)
- PeptideCutter Expasy
- Peptide Fingerprinting at IGH (France)
- Peptide Mass Expasy (chemical or enzymatic cleavage)
- PepStats UMMS (USA)
- PESTFIND (find PEST (proline, glutamic acid, serine and threonin)) Pasteur, see also advanced form (French), see also EMBnet (Austria)
- PI2PE (protein interface/interior prediction engine) Florida (USA)
- PolyPhen (predicts possible impact of an amino acid substitution on the structure and function of a human protein) EMBL (Germany)
- PredAcc (protein side chains relative solvent accessibility) Jussieu (French)
- Profiles (Hopp, Kyte, Karplus, Parker, Argos) PBIL (France)
- Protein solubility (sequence based prediction and experimental verification) Munchen (Germany)
- PROTEOL (Digestion protéolytique d'une protéine) InfoBioGen (Hong Kong)
- ProtParam Expasy (MW, pI, amino acid composition, extinction coefficients, instability and aliphatic index)
- ProtScale Expasy (Compute and represent the profile produced by any amino acid scale on a selected protein : 50 predefined scales entered from the literature)
- Ramachandran plot Bengalore (India)
- RandSeq : generation of a random protein sequence Expasy
- REPPER (repeats and their periodicities in fibrous proteins) Tubingen (Germany)
- Riche en ... (graphical display of content in selected amino acids) ABIM (in french)
- SAPS (Lausanne) ISREC (analyses proteins for statistically significant features like charge-clusters, repeats, hydrophobic regions, compositional domains etc), see also EBI, see also Pasteur
- SIFT (predictions for what amino acid substitutions will affect protein function) FHCRC (USA)
- SIMPLE (identification of simple sequences) UCL (UK)
- SDPpred (prediction of amino acid residues that determine differences in functional specificity of homologous proteins) Moscow (Russia)
- Volume irregularities in proteins SURVOL (PDB format)
- Prediction of signals and site localisation
- AMPer (database and an automated discovery tool for antimicrobial peptides) Vancouver (Canada)
- APID (agile protein Interaction dataanalyzer) Salamanca (Spain)
- AlgPred (prediction of allergenic proteins and mapping of IgE epitopes) Chandigarh (India), another link
- Anagram (protein function assignment) Malaga (Spain)
- AutoMotif (prediction of single residue post-translational modifications in proteins) Poznan (Poland)
- Auto-mute (accurate prediction of enzyme mutant activity based on a multibody statistical potential) Manassas (USA)
- BaCelLo (a balanced subcellular localization predictor) Bologna (Italy)
- CASVM (SVM-based prediction of caspase substrates cleavage sites) Sydney (Australia)
- ELM (predicting functional sites (described by linear motifs) in eukarytic proteins) Heidelberg (Germany)
- ESLpred (SVM-based method for subcellular localization of eukaryotic proteins using dipeptide composition and PSI-BLAST) Chandigarh (India)
- firestar (prediction of functionally important residues using structural templates and alignment reliability) Madrid (Spain)
- iPSORT (site predictor for N-terminal sorting signals) Tokyo (Japan)
- LOCnet and LOCtarget (sub-cellular localization for structural genomics targets) Columbia (USA)
- LOCSVMPSI (subcellular localization of eukaryotic proteins using SVM and profile of PSI-BLAST) Hefei (China)
- MultiLoc (prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition) Tubingen (Germany)
- P2SL (prediction of protein subcellular localization) Virginia (USA)
- Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers Alberta (Canada)
- PrediSi (prediction of signal peptides and their cleavage positions) Braunschweig (Germany)
- PSLpred (prediction of subcellular localization of bacterial proteins) Chandigarh (India)
- PSORT Tokyo, see also NIBB Server for Analyzing and Predicting Protein Sorting Signals Coded in Amino Acid Sequence (Japan)
- PSORT version II (predicts protein subcellular localization sites from their amino acid sequences) Pasteur (French)
- PSORTb (program for bacterial protein subcellular localization prediction) Burnaby (Canada)
- pTARGET (to predict the subcellular localization of eukaryotic proteins from animal species that include fungi and metazoans) Albany (USA)
- Sequence harmony (detecting functional specificity from alignments) Amsterdam (The Netherlands)
- SH3-Hunter (discovery of SH3 domain interaction sites in proteins) Rome (Italy)
- SherLoc (high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data) Tuebingen (Germany)
- SIGFIND (Signal Peptide Prediction) Heraklion (Greece)
- siteFiNDER|3D (for predicting the location of functional sites in proteins) Yale (USA)
- SLiMDisc (short, linear motif discovery in proteins) Dublin (Ireland)
- SLP-Local (subcellular location predictor based on local features of amino acid sequence) Kyoto (Japan)
- WoLF PSORT (protein localization predictor) Tokyo (Japan)
- Prediction of secondary structure
- AGADIR EMBL (Germany) : predict the helical content of peptides
- AllAll ETH Zurich (surface peptide, break), another link
- BetaTPred (Prediction of ß-turns in proteins using statistical algorithms) Chandigarh (India)
- BetaTurn (improved method for predicting beta-turn using support vector machine) New Jersey (USA)
- Beta-turn types I, II, IV and VIII prediction (neural network) Chandigarh (India)
- BhairPred (prediction of Beta-hairpins in a protein from multiple alignment information using ANN and SVM techniques) Chandigarh (India)
- Biocomputing Tools (FT, SecStr, Pred-TMR, Pred-TMR2, OrienTM, CoPreTHI, Pred-Class, LSQR, SCAR) Athens (Greece)
- Coiled-coil prediction PBIL (French)
- Coiled-coil predictions EMBL (Germany)
- COILS : Prediction of Coiled Coil Regions in Proteins EMBNet
- Consensus Data Mining (CDM) (Protein Secondary Structure Prediction Combining GOR V and Fragment Database Mining (FDM)) Iowa (USA)
- Consensus secondary structure prediction PBIL (France)
- CSSP (identifying sequence regions undergoing conformational change via predicted continuum secondary structure) Queensland (Australia)
- DART (Domain Architecture Retrieval Tool) NCBI (USA)
- Determination of expected protein folds Crete (Greece)
- DICHROWEB (protein secondary structure analyses from circular dichroism spectroscopic data) London (UK)
- DisEMBL (intrinsic protein disorder prediction) EMBL (Germany)
- DISOPRED (prediction of protein disorder) London (UK)
- DSC (Multiple alignment and structure prediction) Pasteur (France)
- DSSPcont (automates protein secondary structure assignment from PDB) Columbia (USA)
- FoldIndex (predicts whether a given protein sequence is intrinsically unfolded) Weizmann (Israel)
- FoldUnfold (prediction of disordered regions in protein chain) Moscow (Russian)
- FoReSST (FOld REcognition from Secondary Structure prediction) NIH (USA)
- FORTE (profile-profile comparison tool for protein fold recognition) Tokyo (Japan)
- Garnier UMMS (USA)
- GlobPlot (exploring disorder or globularity in protein) EMBL (Germany)
- GOR4 (J. Garnier, J.-F. Gibrat, B. Robson) ABS (DCRT-NIH)
- GOR I, II, IV PBIL (France)
- GOR V Iowa (USA)
- Helix-Turn-Helix motif prediction PBIL (France)
- HELIXTURNHELIX Pasteur (France)
- HHpred (homology detection & structure prediction by HMM-HMM comparison) Tubingen (Germany)
- HMM-based Protein Structure Prediction UCSC (USA)
- HMMSTR (Hidden Markov Model based on protein STRucture) RPI (USA)
- HYPROSP II (a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence) Taipei (Taiwan)
- I-Mutant2.0 (predicting stability changes upon mutation from the protein sequence or structure) Bologna (Italy)
- iPDA (integrated protein disorder analyzer) Taipei (Taiwan)
- IUPred (prediction of intrinsically unstructured regions of proteins based on estimated energy content) Budapest (Hungary)
- Jpred (A consensus method for protein secondary structure prediction) Dundee (UK)
- K2d (Prediction from CD spectrum) UGR (Spain)
- KemaDom (domain prediction using kernel machine with local context) Shanghai (China)
- LearnCoil-Histidine Kinase Scoring MIT (USA)
- LearnCoil-VMF (coiled-coil-like regions in viral membrane-fusion proteins) MIT (USA)
- M4T (a comparative protein structure modeling server) New York (USA), see also New York
- MaxSub (evaluates the quality of predicted protein structure models) Beer-Sheva (Israel)
- Multicoil (predicts the location of coiled-coil regions) MIT (USA)
- Multicoil (based on paircoil algorithm) MIT (USA)
- nnPredict UCSF (USA)
- NNSSP (combines nearest-neighbor algorithms and multiple sequence alignment) Pasteur, see also BCM
- NORSp (prediction of non-regular secondary structure) Columbia (USA)
- NPS@ (Network Protein Sequence @nalysis) PBIL (France)
- Paircoil (Predicting Coiled Coils) MIT (USA)
- Paircoil2 (improved prediction of coiled coils from sequence) MIT (USA)
- Pcons.net (protein structure prediction) Stockholm (Sweden)
- PDisorder Softberry (USA)
- PEPCOIL Pasteur (France)
- PEPWHEEL Pasteur (France)
- PHD PBIL (France)
- PI2PE (protein interface/interior prediction engine) Florida (USA)
- POODLE-L (a two-level SVM prediction system for reliably predicting long disordered regions) Tokyo (Japan)
- POODLE-S (predicting protein disorder by using physicochemical features and reduced amino acid set of a position-specific scoring matrix) Tokyo (Japan)
- Porter (accurate server for protein secondary structure prediction - recurrent neural network) Dublin (Ireland)
- PrDOS (prediction of disordered protein regions from amino acid sequence) Tokyo (Japan)
- Predicting the structure of your sequence via 123D threading NCI (USA)
- PredictProtein (MaxHom, EvalSec, PHDSec, PHDacc, PHDhtm, PHDTopits EMBL (Germany), see also Cubic (USA), see also CMBI (The Netherlands)
- PREDATOR Pasteur, see also PBIL, see also IGH
- PreLink (prediction of unfolded segments in a protein sequence based on amino acid composition) Orsay (French)
- Prelude&Fugue (predicting local protein structure, early folding regions and structural weaknesses) Bruxelles (Belgium)
- Prof (Multiple alignment and structure prediction)) Wales (UK)
- PROFbval (predict flexible and rigid residues in proteins) Columbia (USA)
- PROFcon (contact prediction method) Columbia (USA)
- Protein Sequence Analysis (PSFinder, SSP, NNSSP, SSPAL, SSENVID, PDISORDER, GETATOMS, 3d-comp, AbIni3D, MDynSB, HMod3DMM, CYS_REC, 3D-match, 3DmodelFit) SoftBerry (USA)
- (PS)2 (protein structure prediction server) Hsinchu (Taiwan)
- PSA (+ amino acid protein class) BMERC (Boston) (results by e-mail)
- PSIPred server London (UK)
- Quadratic Logistic Secondary Structure Prediction without homologues, with homologues (ABS-DCRT-NIH)
- Ramachandran plot Bengalore (India)
- RONN (neural network technique applied to the detection of natively disordered regions in proteins) Oxford (UK)
- Scooby-domain (prediction of globular domains) Amsterdam (The Netherlands)
- Scratch (Structural Proteomics suite : SSpro, ACCpro, CONpro, DIpro, MUpro, DISpro, DOMpro, CMApro, 3Dpro, ICBS, HMMpro, ...) Irvine (USA)
- SDSC (Protein Structure Homology Modeling Server) San Diego (USA)
- Secondary Structure Prediction (Coils, nnpredict, PSSP) BCM
- Simpa96 (optionally multiple prediction with an alignment) PIBL, see also ABS-NIH (USA)
- SMotif (for structural motifs in proteins) Bangalore (India)
- Spritz (prediction of intrinsically disordered regions in protein sequences using kernel machines) Dublin (Ireland), another link
- Structure Prediction server UCLA-DOE (results by e-mail)
- Structure Prediction server (SOPM, SOPMA, HNN, MLRC, DP, GOR I, II, IV, Predator, Simpa96, Consensus) PBIL (France)
- Structure SNP (StSNP : mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways) Boston (USA)
- Sowhat (predicts distance constraints between amino acids in proteins from the sequence) CBS (Denmark)
- SSCP : predictions for the content of helix, strand, and coil for a given protein using the amino acid composition home page, query : sequence, composition (Heidelberg)
- SSEP (domain: protein domain prediction by alignment of secondary structure elements and profiles) Munich (Germany)
- SSP ou NNSSP (BCM Launcher) BCM (USA)
- SSPRED EMBL (Germany)
- SSPRO (secondary structure prediction based on Bidirectional Recurrent Neural Networks) Scratch (USA)
- Wurst (a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices) Hamburg (Germany)
- YASPIN (secondary structure prediction method using hidden neural networks) Amsterdam (The Netherlands)
- Nuclear regions
- DBS-PRED (predictions of DNA-binding proteins and binding sites) New Delhi (India)
- Phobius (a combined transmembrane topology and signal peptide predictor) Karolinska (Sweden)
- PredictNLS (analysis and determination of Nuclear Localization Signals) Columbia (USA)
- NRSAS (nuclear receptor structure analysis) Nijmegen (The Netherlands)
- NucPred (predicting nuclear localization of proteins) Aarhus (Sweden)
- SubLoc (protein subcellular localization : cytoplasmic, extracellular, mitochondrial and nuclear) Tsinghua (China)
- Specific sites
- AllerTool (for predicting allergenicity and allergic cross-reactivity in proteins) Singapore
- Anagram (protein function assignment) Malaga (Spain)
- ANTIGENIC (finds antigenic sites in proteins) Pasteur (France)
- Antigen design tool GenScript (USA)
- Antigenic peptide prediction Harvard (USA)
- Antigenicity Plot (Hopp and Woods) Bioinformatics
- Antigen Selection Pressure on Immunoglobulin Genes Stanford (USA)
- BindN (tool for efficient prediction of DNA and RNA binding sites in amino acid sequences) Kansas (USA)
- CanPredict (a computational tool for predicting cancer-associated missense mutations) San Francisco (USA)
- CDART (protein homology by domain architecture) NCBI (USA)
- CEP (conformational epitope prediction) Pune (India)
- ChloroP (identification of chloroplast transit peptides and their cleavage sites) CBS (Denmark)
- CSS-Palm (palmitoylation site prediction with a clustering and scoring strategy) Georgia (USA)
- CTLPred (prediction of CTL epitopes crucial in subunit vaccine design) Chandigarh (India)
- CytoSVM (for identification of cytokine-receptor interactions) Xiamen (China)
- DILIMOT (discovery of linear motifs in proteins) EMBL (Germany)
- DIMA (domain interaction map) MIPS (Germany)
- DBS-PRED (predictions of DNA-binding proteins and binding sites) New Delhi (India)
- eF-seek (prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape) Tokyo (Japan)
- EVALLER (for in silico assessment of potential protein allergenicity) Uppsala (Sweden)
- FindMod (potential protein post-translational modifications and potential single amino acid substitutions) Expasy (Switzerland), see also FindPept
- Gibbs Centroid Sampler (for locating conserved elements in biopolymer sequences) Providence (USA)
- GPI Predictor (locating potential GPI-modification sites) IMP (Austria), see also GPI-Plant
- GPI-SOM (identification of GPI anchor attachment signals by a Kohonen self-organizing map) Bern (Switzerland)
- GPS (phosphorylation sites prediction) Anhui (China)
- Glycosee, KinasPhos, Sulfosite (predictions of glycosylation, phosphorylation, sulfation sites) Hsin-Chu (Taiwan)
- HLA Peptide Binding Predictions NIH
- HLA-DR4Pred (prediction of peptides binding with MHC class II allele HLA-DRB1*0401) Chandigarh (India), mirror at Bioinformatics
- iCR (to identify conserved targets of a regulatory protein across the multiple related prokaryotic species) Hyderabad (India)
- IMGT/JunctionAnalysis (to identify and analyse the P, N, and D regions of the junctions of the rearranged immunoglobulin) IMGT (French)
- IPPRED (Interaction Partners Inference) CBiB (French)
- KinasePhos (for identifying protein kinase-specific phosphorylation sites) Chung-Li (Taiwan)
- KinasePhos 2.0 (for identifying protein kinase-specific phosphorylation sites based on sequences and coupling patterns) Hsin-chu (Taiwan)
- KISS (Efficient peptide-MHC-I binding prediction for alleles with few known binders) Ecole des Mines (French)
- MEDock (efficient prediction of ligand binding sites) Taipei (Taiwan), autre lien lien
- MeMo (prediction of protein methylation modifications) Beijing (China)
- MeTaDoR (a comprehensive resource for membrane targeting domains and their host proteins) Chicago (USA)
- MHCPred (prediction for epitopes bind to MHC class I molecules) Compton (UK)
- MULTIPRED (prediction of promiscuous HLA binding peptides) Singapore
- Multi-RELIEF (a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting) Amsterdam (The Netherlands)
- Myristoylator (predicts N-terminal myristoylation of proteins by neural networks) Expasy (Switzerland)
- NetAcet (prediction of N-terminal acetylation sites) CBS (Denmark)
- NetAlign (a web-based tool for comparison of protein interaction networks) Anhui (China)
- NetChop (predictions for cleavage sites of the human proteasome) CBS (Denmark)
- NetPhos (Protein Phosphorylation Prediction) CBS (Denmark)
- NetPhosYeast (prediction of protein phosphorylation sites in yeast) CBS (Denmark)
- NetPicoRNA (Posttranslational cleavage by picornaviral proteases) CBS (Denmark)
- NeuroPred (predicts cleavage sites in neuropeptide precursors and provide the masses of the resulting peptides) Illinois (USA)
- NickPred (prediction of proteolytic sites in a protein structure from the PDB) Manchester (UK)
- Pcleavage (an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences) Chandigarh (India)
- PEPVAC (for multi-epitope vaccine development based on the prediction of supertypic MHC ligands) Harvard (USA)
- PiNAT (create and assess protein networks through molecular characteristics of individual proteins) Columbia (USA)
- PIP (potential interactions of proteins - human, rat and fission yeast) London (UK)
- PLOC (prediction of protein subcellular locations) Kyoto (Japan)
- PMUT (tool for the annotation and prediction of pathological mutations on proteins) Barcelona (Spain)
- POPI (predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties) Hsinchu (Taiwan)
- PRED-BALB/c (prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse) Singapore
- Predictions for GlcNA O-glycosylation sites in Dictyostelium discoideum proteins DictyOGlyc (CBS : Denmark)
- Predictions of mucin type O-glycosylation sites in mammalian proteins NetOglyc (CBS : Denmark)
- Predictions of signal peptide cleavage sites in amino acid sequences from different organisms Signalp V1.1 (CBS : Denmark)
- Predotar (putative mitochondrial and plastid targeting sequences) Genoplante (French)
- PREDEP (MHC Class I epitope prediction) Jerusalem (Israel)
- PRISM (protein interactions by structural matching) Istanbul (Turkey)
- ProPred (predicts MHC Class-II binding regions) Chandigarh, see also propred1 (India)
- Proust (predicts positions in the alignment and particular amino acids in them that confer the specific types) EMBL (Germany)
- Prowler (prediction of subcellular localization using sequence-biased recurrent networks) Queensland (Australia)
- Rankpep (predicts MHC binding peptides from an input protein based on their similarity to a set of peptides known to bind to a given MHC molecule) Harvard (USA)
- RASPODOM (rapid motif-based prediction of circular permutations in multi-domain proteins) Munster (Germany)
- REMUS (identification of unique peptide segments as epitopes) Taiwan
- RNABindR (for analyzing and predicting RNA-binding sites in proteins) Iowa (USA)
- SIGCLEAVE (signal cleavage sites) Pasteur (France), see also UMMS (USA)
- SiteEngines (recognition and comparison of binding sites and protein-protein interfaces) Tel Aviv (Israel)
- SoDA (implementation of a 3D alignment algorithm for inference of antigen receptor recombinations) Durham (USA)
- STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) EMBL (Germany)
- Sulfinator (predicts tyrosine sulfation sites) Expasy (Switzerland)
- SUMOsp (sumoylation site prediction) Atlanta (USA)
- SVMHC (prediction tool for MHC I binding) Stockolm (Sweden)
- SVMHC (prediction of MHC-binding peptides) Tubingen (Germany)
- SWAKK (for detecting positive selection in proteins using a sliding window substitution rate analysis) Princeton (USA)
- TargetP (predicts the subcellular location of eukaryotic protein sequences) CBS (Denmark)
- TRANSCOUT (detection and evaluation of conserved motifs in prokaryotic and eukaryotic sequences of proteins with a gene regulatory function) Barcelona (Spain)
- TreeDet (predicting functional residues in protein sequence alignments) Madrid (Spain)
- TSEMA (interactive prediction of protein pairings between interacting families) Barcelona (Spain)
- WebAllergen (for predicting allergenic proteins) Singapore
- 2ZIP (Leucine Zipper Prediction) TBI (Germany)
- ZiFiT (an engineered zinc finger/target site design tool) Iowa (USA)
- Transmembrane regions
- ConPred II (a consensus prediction method for obtaining transmembrane topology models with high reliability) Hirosaki (Japan)
- DAS Stockholm (Sweden)
- DAS-TMfilter Budapest (Hungary), mirror site
- GOLGI (Prediction of Golgi Type II membrane proteins based on their transmembrane domains) Queensland (Australia)
- HHrep (de novo protein repeat detection and the origin of TIM barrels) Tubingen (Germany)
- HMMTOP Budapest (Hungarian)
- Localizome (for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information) Daejeon (Korea)
- MINNOU (enhanced recognition of protein transmembrane domains with prediction-based structural profiles) Cincinnati (USA)
- PHAT (Sequence Comparison for Transmembrane Sequences) FHCRC (USA)
- PHDhtm (transmembrane helix prediction) PBIL (French)
- Phobius (a combined transmembrane topology and signal peptide predictor) Karolinska (Sweden)
- PONGO (multiple predictions of all-alpha transmembrane proteins) Bologna (Italy)
- Prediction tools (HMM-TM, Pred-TMMB, PredSL, MCMBB, orienTM, Pred-TMR, coPreTHi, waveTM) Athens (Greece)
- PRED-TMBB (predicts the topology of beta-barrel outer membrane proteins) Athens (Greece)
- PredTmr (predicts transmembrane segment in proteins) Athens (Greece)
- PROFtmb (predicting bacterial transmembrane beta barrel proteins) Columbia (USA)
- ProperTM (analysis and prediction of buried and exposed faces of transmembrane domain proteins) Cornell (USA)
- PSIPred server (MEMSAT) London (UK)
- SPLIT (Membrane Protein Secondary Structure Prediction) Spli (Croatia)
- TMAP MBB (Sweden)
- TMAP Pasteur (France)
- TMBETA-NET (discrimination and prediction of membrane spanning beta-strands in outer membrane proteins) Tokyo (Japan)
- TMB-Hunt (to screen sequence sets for transmembrane beta-barrel proteins) Leeds (UK)
- TMDET (detection of transmembrane regions by using 3D structure of proteins) Budapest (Hungary)
- TMHMM (V2.0) CBS (Denmark)
- TMLOPP (a combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops) Swansea (UK)
- TMMOD (hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes) Newark (USA)
- TMPred ISREC (prediction of membrane-spanning regions and their orientation by statistical analysis of TMbase)
- TMpro (transmembrane helix prediction through amino acid property analysis) Pittsburgh (USA)
- TMSTAT (Statistical analysis of transmembrane sequences) Yale (USA)
- TopPred 2 (orientation and location of transmembrane helixes) Pasteur
- TRAMPLE (the transmembrane protein labelling environment) Bologna (Italy)
- transFold (predicting the structure and residue contacts of transmembrane beta-barrels) Boston (USA)
- Transmembrane helical topolgy (THUMBUP, THUMBUP-SP, UMDHMM, TUPS) Buffalo (USA)
- TSEG (Prediction Tool for Transmembrane SEGment in Proteins) Kyoto (Japan)
- SOSUI TUAT (Japan)
- Structure 3D
- 3D-JIGSAW (builds three-dimensional models for proteins based on homologues of known structure) BMM (UK)
- 3D-partner (to infer interacting partners and binding models) Hsinchu (Taiwan)
- 3D-PSSM (Protein Fold Recognition (former Foldfit)) BMM (UK)
- 3dLOGO (for the identification, analysis and use of conserved protein substructures) Roma (Italy)
- 3dSS (3D structural superposition) Bangalore (India)
- ArchPRED (a template based loop structure prediction) New York (USA)
- Bioinbgu (fold-recognition based on Sequence-Derived Properties) Ben Gourion (Israel)
- Biozon (prediction of protein domains) Ithaca (USA)
- CASTp (provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities) Illinois (USA)
- CE-MC (Multiple protein structure alignment) Albany (USA)
- CheckHBond (analysing the ability to retain sidechain hydrogen-bonds in mutant proteins) London (UK)
- ClusPro (Filtering, Clustering, and Ranking Protein-Protein Complexes) Boston (USA)
- ClusProt (spatial clusters in protein structures on the basis of atomic contacts between residues) Home page, query PDB sequences only (Heidelberg)
- CODA (Predicting Loops in Protein Structure) Cambridge (UK)
- Confmat (side chain packing optimization) Pasteur (France)
- COMPARER (protein structure superposition from PDB files) Cambridge (UK)
- ConSurf (Identification of Functional Regions in Proteins by Surface-Mapping of Phylogenetic Information) Tel Aviv (Israel)
- CrystTwiV (for automated phase extension and refinement in X-ray crystallography) Athens (Greece)
- CSR (Maximal Common 3D Substructure Searching) Pasteur (France)
- CUPSAT (prediction of protein stability upon point mutations) Cologne (Germany)
- DALI Server EBI (UK)
- DFprot (predicting local chain deformability) Madrid (Spain)
- Dipol (dipole moments of proteins) Weizmann (Israel)
- DSSP (Definition of secondary structure of proteins given a set of 3D coordinates) CMBI, see also Pasteur
- DSSPcont (automates protein secondary structure assignment from PDB) Columbia (USA)
- Domain Assignment BMM (UK)
- DomainParser ORNL (USA)
- DynDom (protein domain motion analysis) Norwich (UK)
- eF-seek (prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape) Tokyo (Japan)
- Environ (accessible as well and buried surface area) Pasteur (France)
- ESyPred3D Namur (Belgium)
- FastContact (a free energy scoring tool for protein-protein complex structures) Pittsburgh (USA)
- fastSCOP (for recognizing protein structural domains and SCOP superfamilies) Hsinchu (Taiwan)
- FATCAT (for flexible structure comparison and structure similarity searching) La Jolla (USA)
- firestar (prediction of functionally important residues using structural templates and alignment reliability) Madrid (Spain)
- Fold prediction 3D (based on homologous sequence search) EMBL (Germany)
- FOLDpro (protein fold recognition and template-based 3D structure prediction) California (USA)
- FoldX (calculating the folding pathways of proteins and the effect of a point mutation on the stability of a protein) Heidelberg (Germany)
- FROST (fold recognition program) INRA (French)
- Fugue (Profile Library Search Against HOMSTRAD) Cambridge (UK)
- GENO3D (Automatic modeling of protein three-dimensional structure) PBIL (French)
- GETAREA (Calculation of Solvent Accessible Surface Areas, Atomic Solvation Energies and Their Gradients for Macromolecules) SCSB (USA)
- GRAMM-X (public web server for protein-protein docking) Kansas (USA)
- HBPRINT (Detection of hydrogen-bond signature patterns in protein families) Bangalore (India)
- HIT (helix interaction tool ) Yale (USA)
- HTHquery (detecting DNA-binding proteins with a helix-turn-helix structural motif) EBI (UK)
- iFold (a platform for interactive folding simulations of proteins) North Carolina (USA)
- iMolTalk (Structural Bioinformatics Toolkit : Structure Alignment, Ramachandran plot, Distance matrix of Cα atoms, Contacts ..) Lausanne (Switzerland)
- InterPreTS (protein Interaction Prediction through Tertiary Structure) EMBL (Germany)
- InterProSurf (for predicting interacting sites on protein surfaces) Institut Curie (French)
- kinDOCK (a tool for comparative docking of protein kinase ligands) Montpellier (French)
- LOOPP (aligns sequence to sequence, sequence to structure, and structure to structure) Cornell (USA)
- MATRAS (protein 3D structure comparison) Nara (Japan)
- MaxSprout (generating protein backbone and side chain co-ordinates from a C(alpha) trace) EBI (UK)
- meta-PPISP (for protein-protein interaction site prediction built on three individual web servers: cons-PPISP, Promate, and PINUP) Florida (USA)
- MinActionPath (maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape) Pasteur (French)
- MODPROPEP (for knowledge-based modeling of protein-peptide complexes) New Delhi (India)
- MONSTER (inferring non-covalent interactions in macromolecular structures) Northwestern (USA)
- ModLoop (modeling of loops in protein structures) UCSF (USA)
- MoViES (molecular vibrations evaluation for analysis of fluctuational dynamics of proteins and nucleic acids) BIDD (Singapore)
- NCI (tool to identify non-canonical interactions in protein structures) Cambridge (UK)
- nsSNPAnalyzer (identifying disease-associated nonsynonymous single nucleotide polymorphisms) Tennessee (USA)
- Pairwise Superposition of Protein 3D Structures CIGB (Cuba)
- PAR-3D (to predict protein active site residues) New Dehli (India)
- PAST (fast structure-based searching in the PDB) Garching (Germany)
- Patch Finder Plus (PFplus : for extracting and displaying positive electrostatic patches on protein surfaces) Haifa (Israel)
- P-cats (prediction of catalytic residues in proteins from their tertiary structures) Tokyo (Japan)
- PDB2PQR (an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations) Washington (USA)
- pdbFun (mass selection and fast comparison of annotated PDB residues) Rome (Italy)
- PDBSiteScan (searching for active, binding and posttranslational modification sites in the 3D structures of proteins) Novosibirsk (Russia)
- Pepitope (epitope mapping from affinity-selected peptides) Tel Aviv (Israel)
- PINTS (patterns in non-homologous tertiary structures) EMBL (Germany)
- Poisson Index (a new probabilistic model for protein-ligand binding site similarity) Leeds (UK)
- POPSCOMP (an automated interaction analysis of biomolecular complexes) Amsterdam (The Netherlands)
- PPI-PRED (an improved prediction of protein-protein binding sites using a support vector machines approach) Leeds (UK)
- PreBI (prediction of biological interfaces of proteins in crystals) Osaka (Japan)
- PreDs (predicting dsDNA-binding site on protein molecular surfaces) Osaka (Japan)
- Pride (efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm) Szeged (Hungary)
- PrISM_Loop (modeling protein loops with knowledge-based prediction of sequence-structure alignment) Taipei (Taiwan)
- ProMateus (an open research approach to protein-binding sites analysis) Rehovot (Israel)
- ProteinDBS (a real-time retrieval system for protein structure comparison) Missouri (USA)
- Protein knot server (detection of knots in protein structures) MIT (USA)
- Protein Peeling (an approach for splitting a 3D protein structure into compact fragments) Jussieu (French)
- ProteMiner-SSM (search for structural motifs) Taipei (Taiwan)
- Protemot (prediction of protein binding sites with automatically extracted geometrical templates) Taipei (Taiwan)
- PROVAT (a tool for Voronoi tessellation analysis of protein structures and complexes) Cambridge (UK)
- Qgrid (clustering tool for detecting charged and hydrophobic regions in proteins) Iizuka (Japan)
- RCI (rapid and accurate calculation of protein flexibility using chemical shifts) Alberta (Canada)
- Residue-rotamer-reduction algorithm for the protein side-chain conformation problem Illinois (USA)
- RosettaDesign (for protein design) North Carolina (USA)
- RPFOLD Chandigarh (India)
- SABBAC (Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace) Jussieu (French)
- Search for common SARFs (Spatial ARangement of backbone Fragments) in protein structures NCI (Comparison of two protein structures by searching common structure (LRS), comparison of a sequence with LRS)
- SCide (identification of stabilization centers in proteins) Budapest (Hungary)
- SCit (tools for protein side chain conformation analysis and editing) Jussieu (French)
- SCMF (Homology Modelling Program) Pasteur (French)
- SHARP2 (protein-protein interaction predictions using patch analysis) Brighton (UK)
- Site-Scan (binding site) Stanford (USA)
- SRide (for identifying stabilizing residues in proteins) Budapest (Hungary)
- STING Contacts (for identification and analysis of amino acid contacts within protein structure and across protein interfaces) Campinas (Brazil)
- STRIDE (search secondary structures in proteins from atomic coordinates) : Pasteur, see also Freising (Germany)
- SuMo (screen the Protein Data Bank (PDB) for finding ligand binding sites matching your protein structure or inversely) PBIL (French)
- SuperPose (for sophisticated structural superposition) Alberta (Canada)
- SWAKK (for detecting positive selection in proteins using a sliding window substitution rate analysis) Princeton (USA)
- Swiss-Model Expasy (An Automated Knowledge-based Protein Modelling based on Blast, Fasta, Sim, CompAli, ProMod and CHARMm)
- Swiss-Model 7TM Interface Expasy (Switzerland)
- TarFisDock (for identifying drug targets with docking approach) Shanghai (China)
- TUNE (Threading Using Neural nEtwork) : the measure of protein sequence-structure compatibility MRC (UK)
- URMS (program for 3-D protein structure comparison) Cornell (USA)
- VAST (Vector Alignment Search Tool) NCBI (USA)
- XtalPred (for prediction of protein crystallizability) Limanowskiego (Poland)
- Alignments
- ALIGN (alignment of 2 sequences : fasta) IGHM (France)
- Align Two Polypeptide Chains by Combinatorial Extension SDSC (USA)
- Align two sequences USC (USA)
- Alignment Comparison UCSC, see also dna-rna
- Alignment Tools (Pasting, Inter-block, Consensus, Clustalw) EMBL-Bork (Germany)
- ALion (Pairwise protein sequence alignment using Needleman-Wunsch or Smith-Waterman algorithms) Stanford (USA)
- AliWABA (alignment through an A-Bruijn approach) California (USA)
- AllAll old-ETH, ,see also ETH (Switzerland)
- AltAVisT (Alternative Alignment Visualization Tool) Bielefeld (Germany)
- AMAS (read an alignment to enhance conserved aminoacids) Barton group (UK)
- APDB (to evaluate the accuracy of sequence alignments using structural information) Marseille (French)
- ARTS (for aligning RNA tertiary structures) Tel Aviv (Israel)
- Bellerophon (detects chimeric sequences in multiple sequence alignments) Brisbane (Australia)
- Blast 2 sequences (alignment using blast) NCBI, see also Pasteur, see also Toulouse
- BLock Gap Sizes (calculates inter-block gap sizes for blocks in a CLUSTAL multiple alignment) EMBL (Germany)
- CBA (consistency based alignment (3D)) Stanford (USA)
- Clustalw
- Clustalw 1.6
- Clustalw 1.7
- Clustalw 1.8
- Clustal W and Clustal X version 2.0
- ComAlign: Combining many multiple alignments in one improved alignment Pasteur (French)
- COMPASS (for remote homology inference) Dallas (USA)
- Consensus (calculates the consensus for the CLUSTAL or MSF multiple alignment) EMBL (Germany)
- Consensus (alignment for reliable framework prediction in homology modeling) Boston (USA)
- CONTRAlign (conditional training for two protein sequences alignment) Stanford (USA)
- COSA (clustal ouput structural analysis (T. Rose)) Pasteur (French)
- CRASP (Correlation Analysis of Sequences of Proteins) MBS (Russia)
- DBA (Dna Block Aligner) EBI (UK)
- DbClustal (Align your Protein to the Blast Top Sequences found in SPtrEMBL) Strasbourg (French)
- DCA (Divide-and-Conquer Multiple Sequence Alignment Bielefeld (Germany)
- DIAL (for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities) Boston (USA)
- DIALIGN Bielefeld (Germany), see also Pasteur (French)
- DomainOrganizer (organization within repeated DNA sequences: application to the study of a family of transposable elements) Rennes (French)
- DRUID (localization of recombination breakpoints in an alignment of sequences) Pasteur (French)
- DSC (Multiple alignment and structure prediction) ICRF (UK)
- eProbalign (generation and manipulation of multiple sequence alignments using partition function posterior probabilities) New Jersey (USA)
- EST2GENOME (align EST and genomic DNA sequences) Pasteur (France)
- ESTScan EMBNet, see V2
- Expresso (automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee) Marseille (French)
- Filtersites (Filter conserved sites in an alignment) Pasteur (French)
- FoldAlign (pairwise local structural alignment of RNA sequences with sequence similarity less than 40%) Frederiksberg (Denmark)
- GLASS (tool for aligning pairs of homologous sequences) MIT (USA)
- GraphAlign NMSU (USA)
- HYPERMUT (detecting hypermutations in viral sequences with an emphasis on G -> A hypermutation) LANL (USA)
- iRMSD (a local measure of sequence alignment accuracy using structural information) Marseille (French), another link
- ITERALIGNv1.1 (multiple alignment of protein sequences) Stanford (USA)
- K2 (protein structure alignment program) ZLab (USA)
- Kalign, Kalignvu and Mumsa (multiple sequence alignment) Stockholm (Sweden)
- LAGAN Alignment Toolkit (Lagan, M-Lagan, Chaos) Stanford (USA)
- LALIGN (alignment of 2 sequences) CRBM (France), see also EMBNet, see also Virginia
- LAMA (Local Alignment of Multiple Alignments: Block vs Block Searcher) FHCRC (USA)
- LGA (method for finding 3D similarities in protein structures) California (USA)
- MAFFT (multiple sequence alignment program) Fukuoka (Japan)
- MAGOS (multiple alignment and modelling server) IBCP (French)
- MAMMOTH-mult (progressive-iterative algorithm for multiple structure alignment) Madrid (Spain)
- MAP2 (multiple alignment of syntenic genomic sequences) Iowa (USA)
- MARNA (multiple alignment of RNAs) Jena (Germany)
- MASS (multiple alignment by secondary structures) Tel Aviv (Israel)
- Match-Box server FUNDP (Belgium), results by e-mail
- MATCHER (inds the best local alignments between two sequences) Pasteur (France)
- MatrixPlot (generate mutual information plots of sequence alignments) CBS (Denmark)
- MAVID/AMAP (multiple alignment) Berkeley (USA)
- MAVL/StickWRLD (analyzing structural constraints using interpositional dependencies in biomolecular sequence alignments) Ohio (USA)
- MGAlignIt (align mRNA sequences to genomic sequences) Singapore
- MMM (a sequence-to-structure alignment protocol) New York (USA)
- MSA (multiple sequence alignment) IGH (French)
- MULALBLA (Multiple alignment with Blast) U-ParisSud (French)
- Multalin PBIL (France)
- Multalin Toulouse (French)
- Multiple alignement (GeneBee) Moscou
- Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC Gottingen (Germany)
- Multiple Sequence Alignment (MAP) Michigan (USA)
- Multiple Sequence Alignments (Clustalw1.8, Map, Pima, Block Maker, Meme, MatchBox) BCM Launcher
- Multiple sequence alignment with user-defined constraints Göttingen (Germany)
- MUSCLE (multiple alignment program for protein sequences) Berkeley (USA)
- MuSiC (tool for multiple sequence alignment with constraints) NCTU (Taiwan), see also MuSiC-ME
- RE-MuSiC (tool for multiple sequence alignment with regular expression constraints) Hsinchu (Taiwan)
- NEEDLE (Needleman-Wunsch global alignment) Pasteur (France)
- Nomad (neighborhood optimization for multiple alignment discovery) Expasy (Switzerland)
- NdPASA (a pairwise sequence alignment server for distantly related proteins) Philadelphia (USA)
- Pair-wise and multiple alignment of genomic sequences using CHAOS and DIALIGN Gottingen (Germany)
- Pairwise Sequence Alignment (SIM, GAP, NAP) Michigan (USA)
- Pairwise Sequence Alignment (SIM, ALIGN, BLAST, LAP2, PCWISE, PCWISE) BCM
- Pairwise Sequence Alignment (Bayesian Algorithm) RPI (USA)
- PAL2NAL (robust conversion of protein sequence alignments into the corresponding codon alignments) EMBL (Germany)
- PARALIGN (rapid and sensitive sequence similarity searches : Smith-Waterman and ParAlign algorithms) Oslo (Norway)
- PIMA (Align a Query Sequence against a PIMA Multiple Alignment using PIMA) BCM
- PIMA (Pattern-Induced Multi-sequence Alignment program) Pasteur (French)
- PipMaker and Multi-PipMaker (alignments of similar regions in two DNA sequences, or more) Pennsylvania (USA)
- PLALIGN (alignment of 2 sequences) Virginia
- POSA (multiple flexible structure alignment (PDB) using partial order graphs) La Jolla (USA)
- Praline (Multiple Sequence Alignment with many options) Amsterdam (The Netherlands)
- PROMALS (towards accurate multiple sequence alignments of distantly related proteins) Dallas (USA)
- PROTOGENE (turning amino acid alignments into bona fide CDS nucleotide alignments) Marseille (French)
- PRSS (evaluate the significance of a protein or DNA sequence similarity score) EMBNet
- QC-COMP (comparison of profile hidden Markov models for protein families) Newark (USA)
- RevTrans (constructing alignments of coding DNA from aligned amino acid sequences) CBS (Denmark)
- SAM UCSC ( linear hidden Markov model), documentation, see also Pasteur
- SANK_AL (statistical evaluation and comparison of a pairwise alignment algorithm that a priori assigns the number of gaps rather than employing gap penalties) Murdoch (Australia)
- SCALI (structural core alIgnment of proteins) New York (USA)
- SEA (protein pairwise alignment based on network matching algorithm) California (USA)
- SIM : Alignment Tool for 2 sequences protein sequences, nucleic sequences (Expasy)
- SIM4 (to align cDNA and genomic DNA) PBIL (French)
- SPEM (multiple sequence alignment with sequence profiles and predicted secondary structures) Buffalo (USA) , see also SPEM-3D
- Spidey (mRNA-to-genomic alignment program) NCBI (USA), another link
- Splign (for computing cDNA-to-Genomic, or spliced sequence alignments) NCBI (USA)
- SQUARE (evaluates the reliability of profile-based or fold recognition alignments) Madrid (Spain)
- SSEARCH Pairwise Sequence Alignment PIR (USA)
- SSAS (Secondary Structure Alignment Server) Rutgers (USA)
- SSEA (protein secondary structure alignment) Padova (Italy)
- SSPA - Significant Segment Pair Alignment Stanford (USA)
- STRAL (progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time) Dusseldorf (Germany)
- STRETCHER (finds the best global alignment between two sequences) Pasteur (France)
- SUPERMATCHER (finds a match of a large sequence against one or more sequences) Pasteur (France)
- T-COFFEE (Multiple Alignments) EMBNET, see aslo IGS
- ToPLign (standard pairwise and multiple alignment methods) GMD (Germany)
- TreeDet (predicting functional residues in protein sequence alignments) Madrid (Spain)
- VerAlign (multiple sequence alignment comparison) Amsterdam (The Netherlands)
- Vorolign (fast structural alignment using Voronoi contacts) Munich (Germany)
- WATER (Smith-Waterman local alignment) Pasteur (French)
- WebVar (rapid estimation of relative site variability from multiple sequence alignments) Milano (Italy)
- WORDMATCH (finds all exact matches of a given size between 2 DNA sequences) Pasteur (France)
- YASS (local alignment of DNA sequences) LIFL (French)
- Phylogeny - Evolution
- AllAll (see also TreeGen) ETH Zurich
- BAMBE (Bayesian Analysis in Molecular Biology and Evolution) Pasteur (France), see also Duquesne (USA)
- Bayesian Phylogenetic Footprint Wadsworth (USA)
- BIONJ (an improved version of the NJ algorithm) Pasteur (France)
- BLASTO (a tool for searching orthologous groups) Princeton (USA)
- Congruence index for testing topological similarity between trees Orsay (French)
- CVTree (a phylogenetic tree reconstruction tool based on whole genomes) Beijing (China)
- Datamonkey (rapid detection of selective pressure on individual sites of codon alignments) California (USA)
- FGF (Fishing Gene Family in a whole genome database) Beijing(China)
- FastDNAml Pasteur, see also advanced form
- FootPrinter (designed for phylogenetic footprinting) Washington (USA)
- FootPrinter3 (phylogenetic footprinting in partially alignable sequences) Montreal (Canada)
- Gblocks (eliminates poorly aligned positions and divergent regions of a DNA or protein alignment for phylogenetic analysis) Barcelona (Spain)
- Identification and measurement of neighbor-dependent nucleotide substitution processes Berlin (Germany)
- iTOL (interactive Tree Of Life : an online tool for phylogenetic tree display and annotation) EMBL (Germany)
- LVB (Reconstructing Evolution With Parsimony And Simulated Annealing) Pasteur (French)
- MicroFootPrinter (a tool for phylogenetic footprinting in prokaryotic genomes) Washington (USA)
- Molphy (ProtML, NucML) Pasteur (France)
- OrthologID (identifies orthologous groups) New York (USA)
- Phylemon (a suite of web-tools for molecular evolution, phylogenetics and phylogenomics) Valencia (Spain)
- PhyloBLAST (facilitating phylogenetic analysis of BLAST results) Vancouver (Canada)
- Phyloblock (align sequences and build a tree) ANL (USA)
- Phylodendron (phylogenetic tree printer) IUBIO (USA)
- PhyloDome (visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets) Vienna (Austria)
- Phyloquart (parciquart, distquart, qstar, addquart) Pasteur (France)
- Phylogenetic tree prediction (from an alignment) Moscow
- Phylogenetic Web Profiler GSF (Germany)
- PHYLIP
- PHYML (maximum likelihood-based phylogenetic inference) Montpellier (French)
- PLEX (protein function prediction using the Protein Link EXplorer) Texas (USA)
- POWER (framework for biomolecular phylogenetic analysis) Miaoli (Taiwan)
- Principal Coordinates Analysis Lyon (French)
- Puzzle (Tree reconstruction for sequences by quartet puzzling and maximum likelihood) Pasteur, advanced form (French)
- Pyramids (pyramidal analysis tool for sequence clustering) Pasteur (French)
- QR2 Pasteur (French)
- Quicktree (Rapid reconstruction of phylogenies by the Neighbor-Joining method) Pasteur (French)
- RecPars (Parsimony analysis of DNA sequences) Aarhus (Denmark)
- RETREE (unroot a tree) Pasteur (French)
- RIO (resampled inference of orthologs) St Louis (USA)
- ROSE (Random-model Of Sequence Evolution) Bielefeld (Germany)
- Roundup (a multi-genome repository of orthologs and evolutionary distances) Harvard (USA)
- SeqGen (Simulation of DNA sequence evolution) Pasteur (France)
- SHOT (Shared Ortholog and Gene Order Tree Reconstruction Tool) Heidelberg (Germany)
- SNAP (calculates synonymous and non-synonymous substitution rates based on a set of codon-aligned nucleotide sequences) LANL (USA)
- SplitsTree 2 Bielefeld (Germany)
- The Transformation Distance (A dissimilarity measure based on large mutations) Lille (France)
- TreeDomViewer (a tool for the visualization of phylogeny and protein domain structure) Wageningen (The Netherlands)
- Weighbor (Weighted neighbor joining) Pasteur (France)
Others
- Genetic
- Functional Mapping, Polyploid Mapping Florida (USA)
- GARD (a genetic algorithm for recombination detection) UCSD (USA)
- HAP (haplotype reconstruction from genotype data using imperfect phylogeny) Berkeley (USA)
- HaploBlockFinder Cincinnati (USA)
- IMpRH Web Server INRA
- INDELSCAN (for comparative identification of species-specific and non-species-specific insertion/deletion events) Miaoli (Taiwan)
- LIAN (tests the null hypothesis of linkage equilibrium for multilocus data) Freising (Germany)
- Linkage Web servers Rockfeller (USA)
- MAP-O-MAT (marker-based linkage mapping server) Rutgers (USA)
- PDA (pipeline diversity analysis) Barcelona (Spain)
- Plotting haplotype-specific linkage disequilibrium patterns by extended haplotype homozygosity Neuherberg (Germany)
- RF-DYMHC (detecting the yeast meiotic recombination hotspots and coldspots by random forest model using gapped dinucleotide composition features) Nanjing (China)
- ROBIN (a tool for genome rearrangement of block-interchanges) Hsinchu (Taiwan)
- Selecton 2007 (advanced models for detecting positive and purifying selection using a Bayesian inference approach) Tel Aviv (Israel)
- SNPStats (a tool for the analysis of association studies) Barcelona (Spain)
- APOPTO-CELL (a simulation tool and interactive database for analyzing cellular susceptibility to apoptosis) Dublin (Ireland)
- Augur (a computational pipeline for whole genome microbial surface protein prediction and classification) Giessen (Germany)
- FAF-Drugs (free ADME/tox filtering of compound collections) Jussieu (French)
- Frog (druG 3D conformation generator) Jussieu (French)
- KOBAS (for automated annotation and pathway identification) Beijing (China)
- metaSHARK (interactive exploration of metabolic networks) Leeds (UK)
- Path-A metabolic pathway prediction Alberta (Canada)
- Pathway Hunter Tool (observing local and global properties of metabolic pathways: `load points' and `choke points' in the metabolic networks) Koeln (Germany)
- SePaCS (application for classification of seroreactivity profiles) Saarbrucken (Germany)
- ABS (QL prediction, MUSEQAL, Clustal, GOR4, FoReSST) NIH (USA)
- Alignment Tools (Simmat, Malgen, Malig, Lova, Mgcat) LSI (Spain)
- Automated analysis
- Automated analysis Genequiz (more than 80 organisms) EBI) (UK)
- GQserve - Public GeneQuiz Server EBI (UK)
- TaxPlot (Protein homologs in Complete Microbial / Eukaryotic genomes) NCBI, see also Protein homologs in Complete Microbial / Eukaryotic genomes NCBI (USA)
- All-IN-ONE SEQ-ANALYZER (Homology Search, Protein Analysis, DNA Analysis) Michigan (USA)
- ASTRAL (Compendium for Sequence and Structure Analysis) Berkeley (USA)
- ATGC, plateforme de bioinformatique du LIRMM (PHYML, FastME, STAR, MS ALIGN, MAM) Montpellier (French)
- BABELOMICS (annotation and analysis of groups of genes in high-throughput experiments : FatiScan, FatiGo, FatiWise, Tissue mining tools, Gsea, Marmite) Valencia (Spain)
- Barton Group WWW Server (Amas, Scanps, Amps, Assp, Jpred, ProEST, 3Dee, GOtcha, RHIMS) Dundee (UK)
- BCM Search Launcher (Baylor) BCM entry point (searches, alignments, patterns (Blast, BlastPat, Pima , Beauty, Blitz, Fasta, FastPat, ClustalW, MAP), prediction ...), What's New, see also Batch Client for BCM Search Launcher (Unix, Mac)
- Berkeley Drosophila Tools (Genie, cis-analyst, Promoter, Splice site, Genotator) Berkeley (USA)
- Berkeley Phylogenomics (Protein structure, function, Evolutionary Tree, Homology Model, Multiple alignment ..) Berkeley (USA), another link
- BiBiServ Sequence Analysis Department (Genome Comparison, Alignments, Primer Design, RNA Studio, Evolutionary Relationships, Orhers) Bielefeld (Germany)
- BioInfo3D (C-alpha, FlexProt, MultiProt, Mass, PatchDock, SiteEngine, ARTS) Tel Aviv (Israel)
- Bioinformatics Center (PredictProtein : META-PP, EVA, NLProt, UniqueProt, NORSp, CHOP, PredictNLS, LOCtree, PROFtmb, TMH-Benchmark, DSSPcont) Columbia (USA)
- Bioinformatics research center (Animators, CombAt, distanceP, Foldalign, GeMprospector, Hudson, MatrixPlot, Phy-fi, RecPars, Rateshift, RNA folding, SLASH, StatAl, tmRDB ...) Aarhus (Denmark)
- Bioinformatics resources (DigiNorthern, KaryoReader, Prot2Gene, DNA thermodyn, Blast) Buffalo (USA)
- Biocomputing Tools (FT, SecStr, Pred-TMR, Pred-TMR2, OrienTM, CoPreTHI, Pred-Class, LSQR, SCAR) Athens (Greece)
- BioInformatics & Molecular Analysis Section (HLA Binding Prediction, Promoter Scan, Signal Scan) BIMAS (USA)
- Bioinformatics and Pattern Discovery (Pattern Discovery, Transmembrane discovery) IBM (USA)
- BioInformatics ressources (Restriction mapping, Transcription Factor Site Scan, ORF plotting, Primer selection, Signal sequence cleavage, Garnier, PRINTS, Pretty plot, Translate) UMMS (USA)
- Bioinformatics Services at IFOM (Blast, HMMER, Assembly, EST Machine, SMS, SeWeR, JaMBW) Rome (Italia)
- Bioinformatics Toolkit (Blast, Fasta, Clustalw, PredictProtein, SEWER interface) CMBI (The Netherlands)
- Bioinformatics Toolkit (ClustalW, Muscle, ProbCons, Mafft, Blammer, HHalign, HHrep, PCoils, Repper, TPRpred, Aln2Plot, Quick2D, Alignment viewer, HHpred, Modeller, iMolTalk, Phylip-Neighbor, Clans, Ancescon, Reformat, 6FrameTranslation, Extract_gis, RetrieveSeq, gi2Promoter, Backtranslator) Tubingen (Germany)
- Bioinformatics Tools (Praline, VerAlign, Alicao, AuberGene, Yaspin, SymSSP, SymPRED, Pops, Domain3D, Repro, ScoobyDo, Trust) Amsterdam (The Netherlands)
- Bioinformatics Tools (Meta-Server, P-Sea, TITO, Modeller, SMD, W-Loop, 3D-Evaluation, LEA, SCWRL 2.8) Montpellier (French)
- Bioinformatics Tools (Emboss, Blast, Fasta, Phylip, Clustal, Dialign2, Pratt, HMMER, Primer, MFold, CAP, SAPS) Hong Kong
- Bioinformatics Web (EMBOSS, Phylip, ClustalW, fastdnaml) Indiana (USA)
- BioI@Sista (Maran, AQBC, Intergenic select, MotifSampler, MotifScanner, ModuleSearcher, Go4G, Toucan) Leuven (Belgium)
- Biological programs accessible through the Web server of Pasteur (France)
- Biomolecular Modelling Laboratory (Sawted, Pip, 3D-PSSM, Prof, Domains, 3D-JIGSAW, Domain Fishing) BMM (UK)
- BioWWW (Codontree, Patscan, UTRscan, Wordup, Markov) Bari (Italy)
- The Brutlag Bioinformatics group (emotif, ematrix, 3motif) Stanford (USA)
- Calculations (Sequence utilities, Translation, rare codons, PCR, Spectro, Bacteria growth, ..) at MolBiol (Russia)
- CBC protein analysis (PANAL : Prosite, Blocks, Prints, Pfam, Smart, Tigrfam) CBC (USA)
- CBSU Web Computing Resources (GenomeSeqAlign, Loopp, Mdiv, Modeller, Moil, MrBayes, P-Blast, P-ClustalW, P-HMMER, P-IprsScan, RepeatFinder, RetrieveSeq, URMS) Cornell (USA)
- Comparative genomics (ECR Browser, Genome Alignment , SynoR, Mulan, zPicture, multiTF, rVista 2.0, eShadow, Creme 2.0, Array2BIO) LLNL (USA)
- Computational Biochemistry Research Tools ETH old-server (Darwin, AllAll, AllAllDB, MassSearch, MultAlign, NuclPepSearch, PepPepSearch, TreeGen), see also ETH (AllAll, ASAS, Darwin, Evolutionary Analysis, FastaToDarwin, Linear Classification, MassSearch, ParseEMBL, PepPepSearch, Phylogenetic Tree, TreeGen, Vertex Cover)
- Computational Biosciences Tools (Generation, Grail, GrailExp, Pipeline, Domain Parser, Prospect, Mira) Oak Ridge (USA)
- Computational Molecular Biology (transFold : Beta-barrel supersecondary structure prediction, Boltzmann Time Warping, RNAmutants : Energy of k-point mutants of RNA, DIANA : Cysteine oxidation state and disulfide bond connectivity, RNALoss : RNA energy spectrum computation, Dishuffle : RNA dinucleotide shuffle, Boltzmann Alignment : Refined global and local alignments) Boston (USA)
- Computational Services developed and offered by EMBL (Protein Function Analysis, Homology and Similarity, Sequence Analysis, Structural Analysis, System Biology Software, Miscellaneous) EMBL (Germany)
- Computer Programs (NASCA, Complexity, BinomSite, MMSite, ARGO, GArna, ReClus, DNAProp, Protein domain recognition, OligoRep, RGSiteScan, RecGroup, POLIIISCAN, Predicting activities of functional sites in DNA/RNA, CRASP, CRAFT) MBS (Russia)
- CSE on line software (EULER, GRIMM, MGR) UCSD (USA)
- DAVID Bioinformatics Resources (expanded annotation database and novel algorithms to better extract biology from large gene lists) NIH (USA)
- DDBJ Search and analysis (Blast, Fasta, Ssearch, Clustalw, Libra-I) DDBJ (Japan)
- DeCypher server (Tera-Blast, GeneDetective, ClustalW, Target Build, Smith-Waterman, Framesearch, HMM, HMM Framesearch, Profile Search, Profile FrameSearch) Stanford (USA)
- Dragon Genome Explorer (Promoter Search and Gene Regions, Complex systems, Gene and Transcript Signals in DNA and RNA, Transcription Factor Binding Sites) BRUS
- EBI Tool Box EBI, all services EBI, emboss tools
- Expasy tools menu , see also Swiss-Model: Automated Protein Modelling Server
- Expression Profiler (tools for clustering, analysis and visualization of gene expression and other genomic data) EBI (UK)
- Fasta Programs (Fasta, SSearch, FastX/FastY, TFastX/TFastY, FastF/TFastF, FastS/TFastS, LAlign/PLAlign, PRSS/PRFX, Grease, Garnier/Chofas) Virginia (USA)
- FUGE (BOMP, ELM, Ka/Ks, Lipo, ParAlign, Pratt, RegExpMaker, DNA Melting, WEBnm@, XHM) UiB-UiO-NTNU (Norway)
- Galaxie (Blast, Align, HMM : sequence identification through automated phylogenetic analysis) Goteborg (Sweden)
- GeneBee services (AliBee, AliGraf, AliComp, TreeTop, DotHelix, RNA secondary structure prediction, Blast2, Fasta3, ClustalW 1.8) Moscou
- GeneHub-GEPIS (digital expression profiling for normal and cancer tissues based on an integrated gene database) California (USA)
- Genestream (Blast, Fasta, Align, LFasta, LAlign, SSearch, Map ...), IGHM (French)
- GENSTYLE (exploration and analysis of DNA sequences with genomic signature) Jussieu (French)
- Helmholtz Network for Bioinformatics (Sequence Analysis and Retrieval, Genome Annotation, Gene Regulation, Protein Families, Protein Function, Protein Structure, Protein Interaction, Enzymes and Metabolism) HNB (Germany)
- HIV Sequence Database tools ( Gene Cutter, Seq-Convert, Readseq, PeptGen, Gap strip/squeeze alignments, Motif Scan, Primalign, Epilign, HIV/SIV Sequence Locator, HIV-BLAST, N-GLYCOSITE, ENTROPY, Consensus Maker, Synchronize Alignments, FindModel) LANL (USA)
- HMM Applications ( SAM-T02, SAM-T99) UCSC (USA)
- Husar (Gopet, cDNA2, SERpredict, ESTAnnotator, DomainSweep, 2DSweep, ProtSweep, IntegrationMap, IntegrationSeq, miRTaCa) DKFZ (Germany)
- In silico analysis of complete bacterial genomes (PCR, AFLP-PCR and endonuclease restriction) Vitoria-Gasteiz (Spain)
- Intronerator (collection of tools for exploring the molecular biology and genomics of C. elegans) California (USA)
- ISREC Software (PSI-Blast, Profile Search, Pattern Search, Motif Scan, ClustalW, T-Coffee, MAFFT, Jacob, Translator, ESTScan) ISREC (Switzerland)
- ISU server (AAT, GeneSequer, SplicePredictor, MyGV, Diverge, MuSeq Box, Alignment, CAP, CpG Islands, GOR V) Iowa (USA)
- Java-based Molecular Biology Work Bench (Alignment Editor, Pattern Searching, PCR, pI, Oligo, Map, Translate, ..) BBS (Australia)
- Logiciels pour la biologie - softwares (Blast, Clustalw, HMMER, Phylip, fastDNAml, BioNJ, Emboss Package, RepeatMasker, Sputnik) CBiB (French)
- Mass Spectrometry Facility (MS-Fit, MS-Tag, MS-Seq, MS-Pattern, MS-Homology, MS-NonSpecific, MS-Digest, MS-Product, MS-Comp, MS-Isotope, DB-Stat, MS-Bridge) UCSF (USA)
- META PredictProtein server (SWISS-MODEL, SDSC1, Loopp, Superfamily, DAS, JPRED, PHD, PROF, PSIpred, PSSP, SAM-T99, SSpro) Columbia (USA)
- Meta-Server (PDB-Blast, ESyPred3D, GRDB, FFAS03, Sam-T02, Superfamily, INUB, FUGUE2, 3D-PSSM, mGenThreader, psipred, profsec) BLBII (Poland)
- MMTSB (Multiscale Modeling Tools in Structural Biology : CASP4 structures, Structure evaluation, Structure refinement, Loop prediction, Ab initio prediction, Utility Functions, Go Model Builder, CHARMM SBMD, GB/PB Comparison) SRI (USA)
- Modelling WHAT IF Web interface (The Netherlands)
- myHits (devoted to protein domains : Psi-Blast, Pattern, Clustalw, T-Coffee, MSA ..) Lausanne (Switzerland)
- NCBI (PubMed, Entrez, BLAST, BankIt, OMIM, Taxonomy, Structure) NCBI (USA), see also Databases and Tools
- NETASA (Prediction/ analysis tools : Qgrid, TMBeta, RVP-Net, ASA view, DBS-Pred, Netasa) Iizuka (Japan)
- NPS@ (Network Protein Sequence @nalysis) PBIL (France)
- Online Resources (2zip, Align, CINEMA, Elephant, FingerPRINTScan, Nickpred, Pepmapper, Pepseeker, PRINTS BLAST, PTree, Siteseer) Manchester (UK)
- Online Services of the Institute of Enzymology (BiSearch, DAS-TMfilter, HMMTOP, IUPred, PDB_TM, SCPRED, SCIDE, SRide, TMDET, Cysredox, DAS, PSORT-B) Budapest (Hungaria)
- On-line software (ARPAnno, DbW, EMBOSS, GOAnno, Ballast, DbClustal, Rascal, Leon, Clustering, vALId) Strasbourg (French)
- On line tools (HMM-TM, Pred-TMBB, PredSL, MCMBB, Pred-Class, orienTM, Prde-TMR, Pred-Couple, Pred-GPCR, waveTM, CoPreTHi, Pred-TMR2, SecStr, hPATM, TMRPres2D, Non-RED, Dam-Bio, GeneVito, Cast, FT) Athens (Greece)
- The Open-Acces Institute (COMBOSA3D, JaMBW, PeCoP, Savvy, SeWeR, Sequence Extractor, SMS 2) Bioinformatics
- Outils (Blast, PSIBlast, rpsBlast, MegaBlast, blast 2 sequences, MultAlin, FrameD, EugeneHom, EMBOSS, Microarray) Toulouse (French)
- PAPIA (Protein Structure Similarity, Protein Sequence Homology, Protein Sequence Multiple Alignment, Protein Secondary Structure Prediction, TFSEARCH (DNA Transcription Factor Binding Site Prediction)) MBS (Japan)
- PAT (a protein analysis toolkit for integrated biocomputing on the web) Montpellier (French)
- PIR Search and Tools (Text Search, Blast/Fasta, Multiple Alignment, Pairwise Alignment, Composition/Molecular Weight) Georgetown (USA)
- Plant databases and tools (NetGene2, NetPlantGene, Cluster Analysis, SPADS) Plant systems Biology (Belgium)
- Prediction/analysis Tools for protein sequences (Spem, Spem-3D, Thumbup, Thumbup-SP, UMDHMM, Tups, Sparks, Sp3, Scud, Ddomain, Dmonomer, Dloop, Dmutant, Dcomplex, DDNA, MC2, Dogma, Tcd, Trans. State) Buffalo (USA)
- Prediction servers (GenomeAtlas, EasyGene, HMMgene, NetGene2, NetPlantGene, NetStart, NetUTR, Promoter - GenePublisher, OligoWiz - ChloroP, LipoPNetNES, SecretomeP, SignalP, TargetP, TatP - DictyOGlyc, NetAcet, NetCorona, NetCorona, NetOGlyc, NetPhosK, NetPhos, NetPicoRNA, Prop, YinOYang, BepiPred, NetChop, NetCTL, NetMHC, ArchaeaFun, CPHmodels, distanceP, ProtFun, RedHom, TMHMM) CBS (Denmark)
- Programs for Comparison and Recognition of Protein Structures (123D, SARF2, PDP) NCI-FCRDC (USA)
- Protein Folding and Design Group (Agadir, FoldX, Tango) Heidelberg (Allemagne)
- Protein Prospector (MS-Fit, MS-Tag, MS-Seq, MS-Pattern, MS-Homology, MS-NonSpecific, MS-Digest, MS-Product, MS-Comp, MS-Isotope, DB-Stat, MS-Bridge) UCSF (USA), see also Melbourne (Australia)
- Protein Structural Analysis (Secondary structure, Folding, PimaII, Threading) BMERC (USA)
- Protein Structure Prediction (Casp1...Casp7, AL2TS, LGA, SOV) Calfornia (USA)
- Protein structure prediction (PsiPred, GenThreader, MemSat, GTD, DisoPred, DomPred, COPS) London (UK)
- Protein tools (Sbase, Fthom, P450, Pride, CX, DPX) Trieste (Italie)
- PROWL (ProteinInfo, ProFound, PepFrag, GPM) Rockfeller (USA)
- RADAR (for RNA data analysis and research : Structure, sequences...) Frederick (USA)
- RDP-II Online Analyses (Phylip, Probe Match, Sequence Match, Sequence Aligner, Similarity Matrix, Chimera Check, Alignment Slices, T-RFLP, TAP T-RFLP, Sub Trees) CME (USA)
- SAGE (Serial Analysis of Gene Expression) NCBI, see also Sagenet, see also WebSage
- Samuel Karlin Group Web Server (SplicePredictor, ITERALIGN, SSPA, GENSCAN) Stanford (USA)
- SBC services (PRIMETV, Binary Repeat Align Server - Pcons, Pcomb, Pmembr, HMMER, 3D-PSSM, ProQ - PRODIV-TMHMM, DAS, TopPred, TMAP - NucPred - DRIP-PRED, GPCPRED, SVMHC) SBC (Sweden)
- SBNet (Structural Biology Network : BioSEL, ProSAL, HetSEL, ProSal Lite) Uppsala (Sweden)
- SCRATCH (protein structure and structural feature prediction : SSpro, ACCpro, DIpro, MUpro, DISpro, DOMpro, Betapro, CMAPpro, FOLDpro, 3Dpro) California (USA)
- SDSC Biology (WorkBench, Meme, Meta-Meme, Molecular Information Agent, Family Pairwise Search, Conformational Likeness Search, Combinatorial Extension) San Diego (USA)
- Sequence Analysis & Tools at Stanford (USA)
- (Blast, Fasta, Primer, PatMatch, Restriction, SAGE, Similarity View..) S. cerevisiae
- (Blast, Fasta, Primer, PatMatch, Restriction..) Arabidopsis (TAIR)
- Sequence Analysis Server (Finding genes, Pairwise alignment, Multiple alignment) Michigan (USA)
- Sequence Analysis Tools (GPI predictor, Myristoylation predictor, PTS1 peroxisomal signal, SSP, DAS-TMfilter, SAPS, SEG, COIL) Vienne (Austria)
- Sequence Interpretation Tools (Blast, Fasta, Motif, TFSearch, ClustalW, Mafft, PRRN, PSort, SOSUI, TSeg, PLoc, KCaM, EGassembler, KAAS) Kyoto (Japan)
- The Sequence Manipulation Suite (DNA entry, manipulation, figures, analysis - Protein entry, manipulation, figures, analysis) Bioinformatics
- Sequence Tools (Sequence Conversion, Multiple Alignement) TAGC (French)
- Services (Blast, Smith-Waterman, WuBlast, EMBOSS, MarCoil, Coils, SAPS, TmPred, Saps, LAlign, PRSS, BoxShade, ClustalW, T-Coffee, iPCR) at EMBNet (Switzerland)
- Services (Gene finder, Genome search, Promoter, Protein structure, Protein location) at Softberry (USA)
- Services BiophysWWW supplies (DotPlot, Poland, Tinocco, Langmuir, Construct) Dusseldorf (Germany)
- SEWER (Blast, Blocks, Cap, Clustal, GeneMark, Primer, Protein Machine, ProtParam, PsiPred, ScanProsite, Webcutter) Bioinformatics, see also Bari
- Similarity Search Engines ProWeb (USA)
- Software at the Roth Lab (GoFish, ClusterJudge, Complexpander, ChIPper, FuncAssociate) Harvard (USA)
- SPACE (predicting and analyzing structures of biomolecules and their complexes : LPC/CSU, CryCo, CMA, MutaProt, SCCOMP) Weizmann (Israel)
- sgTarget (a target selection resource for structural genomics) York (UK)
- Structural Bioinformatics Group (3D-ID, 3SOM, DisEMBL, PINTS, InterPreTs, Proust, Coiled-coil,) EMBL (Germany)
- Structural Biology on line (Fugue, TraceSuite II, Coda, Petra, Joy, Comparer, Crescendo) Cambridge (UK)
- Structure, Function Prediction sever (Data-Structure, Sequence-Structure, Sequence-Function, Structure-Function) UCLA-DOE (USA)
- SWBIC (BLAST Filter, GraphAlign, PCAPSS, Blast, SeqCheck, SeqMake, SeqEST, EXTNUM) NMSU (USA)
- SWISS-MODEL Workspace (an automated protein structure homology-modeling server) Expasy (Switzerland)
- TBI services (2Zip, Blast, Fasta, Ssmal, GeneNest, MSA, Pride, WebDiffs) DKFZ (Germany)
- TigemNet (GloBlast, SMS2, Blat) TigemNet (Italie)
- Tools for Bioinformatics research (Blast, Electronic PCR, Model Maker, ORF Finder, SAGEMap, Spidey, Splign, VecScreen, CD Search, CDART, OMSSA, ProtEST, TaxPlot, CN3D, Vast Search, COGs, GEO) NCBI (USA)
- Tools Online (SIMP, GIMP, DNannotator, MutScreener) Chicago (USA)
- TOPS (Protein Topology : search, compare, cartoon..) Leeds (UK)
- USF WWW services (SPASM, DEJAVU, HIC-Up, MOLEMAN, MAPMAN, EDS) Uppsala (Sweden)
- VISTA (suite of programs and databases for comparative analysis of genomic sequences) Berkeley (USA)
- WebGene Server (GeneBuilder, RepeatView, CpG, Splice view, HCpolya, HCtata, Genview, AUG) ITBA (Italy)
- Workbench (web-based tool for biologists) SDSC (USA)
- WWW Query PBIL (French)
- Zhang Lab server (ESEfinder, FirstEF, Gene Finder, CorePromoter, PolyA, CpG, MatCompare) CSHL (USA)
- Index
- Analysis tools Pasteur (France)
- DNASYSTEM (Sequence Analysis Site) San Diego (USA)
- Online Analysis Tools Ontario (Canada)
- Similarity Search Engines Proweb (USA)
- Software Seek genamics (USA)
Utilitaries
- BOXSHADE Pretty Printing and Shading of Multiple-Alignment files EMBNet, see alos Pasteur (France)
- Buffers for pH control Manchester (UK)
- CNplot (Visualization of Large scale Clustered Networks) Stanford (USA)
- Drawseq - biosequence drawing tool Indiana (USA)
- Filtersites (Filter conserved sites in an alignment) Pasteur (French)
- Fmtseq (sequence conversion) Pasteur (France)
- GB2xml (Genbank to XML conversion tool) Pasteur
- HARMONY (assessment of protein structures) Bangalore (India)
- JOY (protein sequence-structure representation and analysis) Cambridge (UK)
- Lowercase low-complexity regions (PSEG) Virginia (USA)
- Map2mod (a server for evaluation of crystallographic models and their agreement with electron density maps) Virginia (USA)
- ModelMaker (to construct mRNA sequences from genomic data) NCBI (USA)
- MolProbity (all-atom contacts and structure validation for proteins and nucleic acids) Durham (USA)
- MuSeqBox (Multi-query Sequence Blast output examination) ISU (USA)
- NQ-Flipper (validation and correction of asparagine/glutamine amide rotamers in protein crystal structures) Salzburg (Austria)
- PlasMapper (for drawing and auto-annotating plasmid maps) Alberta (Canada)
- PMG (online generation of high-quality molecular pictures and storyboarded animations) Jussieu (French)
- POLYVIEW (a flexible visualization tool for structural and functional annotations of proteins) Cincinnati (USA)
- ProSA-web (for the recognition of errors in three-dimensional structures of proteins) Salzburg (Austria)
- PTree (PRINTS Tree) Manchester (UK)
- The Protein Colourer EBI (by default, colour aminoacids according to their hydrophobicity : settings change available)
- Query Chem (a Google-powered web search combining text and chemical structures) Harvard (USA)
- Sequence Shuffle (shuffle the order of characters to produce a randomized sequence with the same overall composition) Arizona (USA)
- SHUFFLESEQ (shuffles a set of sequences maintaining composition) Pasteur (France)
- Tools for alignments Heidelberg
- VisCoSe (visualization and comparison of consensus sequences) Muenster (Germany)
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