- Search a sequence database
- Nucleic acids sequences
- Patterns (proteins)
- Prediction on protein sequences
- Alignments - Phylogeny
- Analysis tools package
- Sequence comparison
- BioSCAN
- 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 or EPFL, [D] with extra : analyse and align all HSPs
- IBB (Padoue)
- IGHM (French) [D]
- IGS (French [E]
Databases : NR, Month, SwissProt, Dbest, DBSTS, GBxxx, PDB, Vector, Kabat, NRSub, Transfac ...
- Sanger (Blast and Ssaha : search on a set of protein or nucleotide databases available at the Sanger Centre)
- Strasbourg (Ballast : explore the depths of Blast searches) (French)
- TBI (Germany) [E, P]
- Toulouse (French)
- Search of Anopheles gambiae NCBI (USA)
- Search of Arabidopsis sequence tagged inserts NASC (UK)
- Search of Aspergillus nidulans Oklahoma (USA)
- Search of C. elegans DatabaseSanger, see also St Louis, see also NIG
- 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) : Tsukuba (Japan), see also Jena
- Search of Drosophila : BDGP (Berkeley), see also EBI [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 rubripes : blastp HGMP (UK)
- Search of HIV-1 (subtyping) NCBI (USA)
- Search of Human Sanger (UK), see also St Louis (USA)
- Search of Human (blastn) MIPS, see also EST (Germany)
- Search of Human UCSC (USA)
- Search of Human Repeat Oklahoma (USA)
- Search of "Kegg genome" Kyoto (Japan)
- Search of Immunoglobulins NCBI (USA)
- Search of microbial genomes NCBI (USA)
- Search of M. leprae Sanger (UK)
- Search of M. tuberculosis Sanger (UK) (results by e-mail)
- Search of Neisseria gonorrhoeae Oklahoma (USA)
- Search of OWL BMB, see also UCL (UK)
- Search of P450 Biobase (Denmark)
- Search of Plant knockout databases SDSC (USA)
- Search of Plasmodium Sanbi (South Africa)
- Search of P. falciparum Sanger (UK), see also NCBI
- Search of protein Databank PBIL (French) [S]
- Multiple Custom Databases (P.falciparum, P.vivax, P.berghei, P. chabaudi, EST) NCBI (USA)
- Search of Streptococcus pyogenes Oklahoma (USA)
- Search of S. cerevisiae MIPS (Germany)
- Search of S. pombe Sanger (UK)
- Search of UTR, SwissAll, GenPep, EST, Gss, Htg, Vector Bari (Italy)
- Search of Y. pestis Sanger (UK)
- Search of Zebra fish NCBI (USA)
- Species-Specific Protein Sequence Searches BCM (USA)
- PRINTS Blast Manchester (UK)
- Prodom with Blast Toulouse [D] (French)
- Search of SBASE8.0 Database ICGEB (Trieste) ((results by e-mail), see also ABC
- 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 BMRB Database (BioMagResBank : A database of NMR-derived protein structures) NIH
- Search of NRL_3D PBIL (French) [S]
- Search of Ex-NRL-3D (SWISS-MODEL Blast) Expasy
- Search of Ribosomal RNA (SSU, LSU) Gent (Belgium)
- Swiss 7TM BLAST Expasy
- 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]
- NIMR (USA)
- Pasteur [D]
- Toulouse [D]
- UMMS [E]
- Search of Arabidopsis TAIR, see also St Louis [D, E]
- Search of SBASE8.0 Database ICGEB (Trieste) ((results by e-mail), see also ABC
- Search of NRL_3D or SwissProt PBIL (French) [S]
- Search of microorganisms U-ParisSud (French)
- Search of Plasmodium Sanbi (South Africa)
- 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]
- EMBL (Germany) [D]
- EMBNet [D]
- Submission form to the WU-BLAST server at Lausanne at Expasy (Switzerland) [D], another link
- EMBNet (Switzerland) [D]
- GenomeNet (Japan) [D]
- GSC (USA)
- Manchester (UK)
- Moscou (Russia)
- Pasteur, advanced form [D]
- UMMS (USA) [E]
- Wash-U. multi-processors Pasteur [D]
- Orthologue Blast2 (Finding orthologues & Distinguishing them from paralogues) Heidelberg (Germany)
- Prodom with Blast ProDom [D] (+ graphic display of the domain)
- Search of Arabidopsis 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 SDSC (USA)
- 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 Merops(protease database) Sanger (UK)
- Search of Mouse Jackson (USA)
- Search of Mouse Ensembl
- Search of Parasites CBIL (USA)
- Search of Parasites EBI (UK)
- Search of P. falciparum Sanger (UK), see also Stanford (USA)
- Search of Prokaryotes JGI (USA)
- Search of SBASE8.0 Database ICGEB (Trieste) ((results by e-mail), see also ABC
- Search of S. cerevisiae Stanford (USA) [D, E]
- Search of S. pombe Sanger (UK)
- Search of Salmonella typhi Sanger (UK)
- Search of Zebrafish Ensembl
- Search of dbEST TigemNet (Italy)
- 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
- EBI Cambridge (results by mail)
- Form at IGHM to EMBL (results by mail)
- FASTA
- DISC (Japan) (results by e-mail)
- Fasta3 Cambridge (UK)
- Fasta3 CMBI (Netherlands)
- Fasta3 EBI (UK)
- Fasta33 EBI (UK)
- Fasta3 (TFASTX/TFASTY, FASTF/TFASTF, FASTS/TFASTS) Virginia (USA)
- GenomeNet (Japan)
- IGHM (French)
- Pasteur
- TBI (Germany)
- Search of PIR PIR (USA)
- Search of Arabidopsis TAIR
- Search of C. elegans NIG
- Search of Dictyostelium Tsukuba (Japan)
- 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)
- GenQuest ( choice of BLAST, FASTA, Smith-Waterman)
- Form : IGHM (at John Hopkins)
- ORNL, another link (Oak Ridge)
- 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)
- PDB-ISL (PDBintermediate sequencelibrary)
- ProClust : Protein Clustering - Searching for Homologue Proteins by using transitivity
- Quest (iterative sequence databank search tool)
- RedHom (CPH models : finds a subset with low sequence similarity)
- Smith et Waterman
- Affine Smith-Waterman Algorithm Stanford (USA)
- Bioccelerator Applications Using GCG at Weizmann Institute (Smith-Waterman and ProfileSearch), see also EMBL-Gibson [D]
- Bioccelerator_SW (Smith-Waterman) EBI [D]
- 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 IGS, 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)
- ProtEST (Search the EST database with a protein sequence) EBI 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 (search EMBL, SWISS-PROT) ETHZ (Switzerland)
- Mowse (search OWL) HGMP (UK)
- 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
- Protein identification (ProFound : OWL and PepFrag : GenPept, NRL-2D, PIR, Swiss-Prot) NYC (Rockfeller), see also ressources
- 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
- 3DALIGN Tokyo (Japan)
- 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
- (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)
- GeneFIND Family Identification System PIR (USA)
- 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)
- Kangaroo (pattern search with regular expression) BluePrint
- Metamotif Search ISREC (Switzerland), see also Motif relation
- MOTIF Kyoto (Japan)
- Motifs in protein databases Alces (Yeast, Worm, Human)
- NAIL (Network Analysis Interface for Linking HMMER results) EMBL (Germany)
- PATOSEQ (motif search and alignment program) Expasy
- PatternFind : SwissProt - GenPept (ISREC) Pattern will be written with the Prosite syntax, or with the regular expression (in french) syntax of Perl
- Pattern Match (PIR, NRL_3D, ProClass, PATCHX, FAMBASE) PIR (USA)
- PattinProt (Swissprot, NRL_3D, SP-TREMBL) PBIL (French)
- RAMdb Citi2 (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) San Diego (USA)
- Proteins Alces (Minnesota) search a subset of Genbank, see also
- DNA regular expression BMERC (USA)
- Kangaroo (pattern search with regular expression) BluePrint
- MAST (Motif Alignment and Search Tool) San Diego (see next MEME), see also Stanford (USA), see also Pasteur
- PatMatch (Yeast Genome Pattern Matching
- Pattern search in TRANSFAC GBF (Germany)
- PatScan Argonne (Proteins or Nucleic acids, selection of genomic libraries)
- REPATT & TRANSPO (exact consecutive repeats - transposons) Barcelona (Spain)
- Search for Sequence Pattern (DNA, protein) LBGBP (French)
- SeqhuntII-Match : search the Kabat database for nucleotides or amino acids pattern
- Sig (Multiple Prosite motifs searching) Pasteur (French)
- Signal Scan (search TDF and Transfac for eucaryotic signal) : NIH, or search IMD NIH
- Sequence Assembly
- CAP (Contig Assembly Program Based on Sensitive Detection of Fragment Overlaps) InfoBioGen (French), see also TigemNet (Italy)
- 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 - ...
- Biopolymer calculator Yale (USA)
- 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)
- Codonw (Correspondence Analysis of Codon Usage) Pasteur (French)
- Countcodon Kazusa (Japan)
- CpG islands ITBA (Italy), see also EBI
- CpG rich regions Pasteur, see also plot, see also newcpgseek
- EMBOSS at Pasteur (French), see also EMBOSS at OUBC (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
- Find the linguistic complexity in nucleotide sequences COMPLEX
- Finds MAR/SAR sites in nucleic sequences MARSCAN
- NEFF 1.0 (takes as input the output of a BLAST and computes the SNP-effective) Max-Planck (Germany)
- 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
- GCUA (Graphical Codon Usage Analyser) Regensburg (Germany)
- MSBAR (mutate sequence beyond all recognition) Pasteur (French)
- Riche en ... (graphical display of content in selected bases) ABIM (in french)
- Verbumculus ( over- or under-represented words : suffixe tree) California (USA)
- Map (restriction)
- Arabidopsis Restriction Mapper TAIR (USA)
- Find restriction sites Texas (USA)
- NEBcutter V2.0 BioLabs
- TACG Pasteur (French), see also CMBI
- Webcutter Yale, mirror at Sweden
- Restenzyme Budapest (Hungary)
- RESTRICT (finds restriction enzyme cleavage sites) Pasteur (French)
- Restriction Enzyme Analysis Geneseo (USA)
- Restriction Mapper
- Restriction Site Analysis UMMS (USA)
- RIFLE (16S rDNA-based identification of microorganisms by comparison with RDP database restriction patterns) Bielefeld (Germany)
- SaGa (Structure Analysis with Genetic Algorithms (SaGa) to analyse your aligned sequence set for common structural characteristics) GSF (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)
- Affycomp (benchmark for Affymetrix GeneChip expression measures) Johns Hopkins (USA)
- Affymetrix Data Conversion UCI (USA)
- AMPhora Expression Data Analysis MIPS (Germany)
- Analysis tools NCGR (USA)
- 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)
- CIMMiner (generates color-coded Clustered Image Maps (CIMs) ("heat maps") to represent "high-dimensional" data sets such as gene expression profiles) NCI (USA)
- Clustering, Motif sampler, Intergenic select Sista (Belgium)
- 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)
- DNA Microarray Analysis Tools IGB (USA)
- DNA probe database for DNA Oligo microarray St Louis (USA)
- eXPatGen (Gene Expression Pattern Generator) Newark (USA)
- Express Yourself Yale (USA)
- Expression Profiler (online platform for analysis of microarray data) EBI (UK)
- GAP (Genome- wide Automated Primer) UCI (USA)
- GenePublisher CBS (Denmark)
- GEPAS (pipeline for microarray gene expression data) Madrid (Spain)
- GOAL (automated Gene Ontology analysis of expression profiles) Ferrara (Italy)
- KARMA (application for comparing and annotating heterogeneous microarray platforms) Yale (USA)
- MADTools (analysis and storage data) Nantes (French)
- 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)
- Oligodb (interactive design of oligo DNA for transcription profiling of human genes) Berlin (Germany)
- 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)
- 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)
- 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)
- Consensus (identification of consensus patterns in unaligned DNA and protein sequences) Pasteur (French)
- Emotif (find motifs in aligned sequences) Stanford (USA), see also 3motif
- FUZZNUC (nucleic acid pattern search) Pasteur (French)
- GenCANS-RDP System (classification of small subunit ribosomal RNAs) PIR (USA)
- MEME (tool for discovering motifs in groups of sequences) San Diego, see also Pasteur
- Pattern Scanning with Profiles Max-Planck (Germany)
- Pattern_Search (searching potential composite elements similar to the COMPEL collection) GBF (Russia)
- Scan_for_matches Pasteur (French)
- SMILE (tool that infers motifs in a set of sequences) à Pasteur : simple motif, with 2 boxes
- 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)
- Alces (Minnesota)
- Alces (graphic)
- Aide PCR (in french) Citi2 (French)
- AcePrimer (automation of PCR primer design based on gene structure) Vancouver (Canada)
- AFLPinSilico (simulating AFLP fingerprints) Gent (Belgium)
- AMPLI LSI (Spain)
- AOPredict (Antisense Oligonucleotide Prediction Program) Karolinska (Sweden)
- 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)
- Electronic PCR (PCR-based sequence tagged sites (STSs)) NCBI (USA)
- 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)
- Oligo Calculator (Java script) Pittsburg, see also Adelaide
- Oligo Calculator BioInf (USA)
- Oligodb (interactive design of oligo DNA for transcription profiling of human genes) Berlin (Germany)
- PCR designer for restriction analysis of various types of sequence mutation Oxford (UK)
- PCR primer selection VGC (USA)
- PCR Suite (Overlapping_Primers, Genomic_Primers, SNP_Primers, cDNA_Primers) Rotterdam (The Netherlands)
- PIRA (PCR designer for restriction analysis of single nucleotide polymorphisms) Southampton (UK)
- Plasmid Drawing Tool JIC (UK) (Applet Java)
- PRIDE (PRImer DEsign for large scale sequencing) TBI (Germany)
- 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 Pick V 3 MIT, see also EMBNet
- Primer 3 (new interface) MIT (USA), see also UMMS (USA)
- Primer finder Dallas (USA)
- The Primer Generator Johns Hopkins (USA)
- Primo (Prediction of forward and reverse oligonucleotide Primers) Pasteur (French), see also Texas
- Primo MSP (methylation specific PCR Primer design) Chang Bioscience
- Radiation Hybrid Mapping MIT (USA)
- siDirect (target-specific siRNA design software for mammalian RNA interference) Tokyo (Japan)
- siRNA selector Philadelphia (USA)
- siRNA Design Tool (filtering, ...) Hong Kong (UK)
- SNPbox (primer design from gene to genome) Antwerp (Belgium)
- 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)
- 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)
- AGenDA (gene-prediction tool that is based on cross-species sequence comparison) Bielefeld (Germany)
- Ann-spec (locates common DNA regulatory patterns in a set of promoter region sequences) CBS (Denmark)
- ASmodeler (gene modeling of alternative splicing events) Seoul (Korea)
- ATGpr (identifies the initiation codons in cDNA sequences) HRI (Japan)
- AUG_EVALUATOR (for start codons prediction) ITBA (Italy)
- AUGUSTUS (for gene finding in eukaryotes) Gottingen (Germany)
- Bacterial Promoter, Operon and Gene Finding SoftBerry
- BioProspector (Discovering Conserved DNA Motifs in Upstream Regulatory Regions of Co-Expressed Genes) Stanford (USA)
- BCM Gene Finder (exons, splicing sites, promoter, coding region) BCM, see also Gene Feature Searches
- 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)
- Cister (Cis-element Cluster Finder) Boston (USA)
- Cister (Cis-element Cluster Finder) Boston (USA)
- ConPro (consensus promoter predictor) Michigan (USA)
- ConSite (prediction of regulatory elements using cross-species comparison) Stockholm (Sweden)
- Core-Promoter Finder CSHL (USA)
- Correspondence Analysis Lyon (French)
- CpGProD (CpG Island Promoter Detection) PBIL (French)
- CSTminer (identifies coding and noncoding conserved sequence tags through cross-species genome comparison) Rome (Italy)
- 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)
- Dragon Genome Explorer (Promoter finder, CG+ PF, ATG finder, CpGIslands, Splice sites, PolyA) BRUS
- EcoParse (mailserver for finding genes in E. coli DNA) Info (Denmark)
- E2F transcription factor binding DNA-site EMBNet (Russia)
- Eponine (mammalian transcription start sites) Sanger (UK)
- ESTMAP (tries to predict introns in DNA comparing ESTs and a query sequence) ITBA (Italy)
- Eukaryotic Promoter Prediction by Neural Network Berkeley
- Fast Signal Scan Max-Planck (Germany)
- FirstEF (first-exon and promoter prediction program for human DNA) CSHL (USA)
- FrameD (genes and frameshifts in procaryotic sequences) INRA (French), another link
- FramePlot NIH-NET (Japan)
- FrameShift Error Detection FSED (Marseille)
- 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) GSF (Germany)
- GeneBuilder ITBA (Italy)
- 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)
- Gene Recognition via Spliced Alignment USC (USA)
- Geneid IMIM
- GeneSplicer TIGR (USA)
- Genie (gene finder based on Hidden Markov Models) Berkeley, see also UCSC
- GenLang (tRNA, group I intron, protein gene : "Linguistic Methods") CBIL (Pennsylvania)
- GenomeScan (predicting the locations and exon-intron structures of genes) MIT (USA)
- GeneSeqer (identifies potential exon/intron structure in (plant) pre-mRNA) ZmDB (USA), see also for Arabidopsis 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)
- GenView (Protein-Coding Gene Prediction) ITBA (Italy)
- GRAIL ORNL, another link Oak Ridge (Exons, repeats, Poly A sites, CpG)
- HCpolya (Hamming Clustering poly-A prediction in Eukaryotic Genes) ITBA (Italy)
- HCtata (Hamming-Clustering Method for TATA Signal Prediction in Eukaryotic Genes) ITBA (Italy)
- 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)
- 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)
- Microbial gene prediction ORNL (USA)
- 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)
- 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)
- 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...) Sanger (UK), see also SoftBerry
- ORF Finder (graphical analysis tool) NCBI (USA)
- ORFGene (Gene Structure Prediction using Homologous Proteins) ITBA (Italy)
- 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)
- PolyA signals CSHL (USA)
- PredictGenes (predict and verify gene structure by alignment with homologous proteins) ETHZ (Switzerland)
- PredictRegulon (prediction of the regulatory protein binding sites and operons in prokaryote genomes) EMBnet (India)
- PROMO (identification of putative transcription factor binding sites) LSI (Spain)
- Prokaryotic promoter analysis using SAK London (UK)
- Promoter classification EMBNet (Russia)
- Promoter 2 (vertebrate Pol II promoters) CBS (Denmark)
- Proscan II (predicts putative eukaryotic Pol II promoter sequences) : Minnesota, see also NIH
- 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)
- RESCUE-ESE (identifies candidate exonic splicing enhancers in vertebrate exons) MIT (USA)
- RecSta (coding region (CDS or exon) prediction program using COA) Lyon
- RiceHMM (Gene Prediction Program for Rice) RGP (Japan)
- RNA Genie (locates RNA genes) LBL (USA)
- Search Genes and Coding Regions (CDS, Xpound, Genescan, Genemark, GRAIL, MORGAN, GLIMMER) Pasteur (French)
- SGP-1 (homology based gene prediction program) Max-Planck (Germany)
- ShiftDetector (detection of shift mutations) Volcani (Israel)
- SITECON (tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition) Novosibirsk (Russia)
- SPADS (Specific Primer and Amplicon Design Software) Genoplante (French)
- SplicePredictor (identifies potential splice sites in (plant) pre-mRNA) ZmDB (USA)
- SpliceProximalCheck EBI (UK)
- Splice Site Prediction by Neural Network Berkeley (USA)
- SpliceView (Splice Prediction by using Consensus Sequences) ITBA (Italy)
- STRING (Search Tool for Recurring Instances of Neighbouring Genes) EMBL (Germany)
- Suite of web-based programs to search for transcriptional regulatory motifs (BioProspector, CompareProspector, MDscan) Stanford (USA)
- SynCod (a computing system for CDS prediction based on BLASTN output) ITBA (Italy)
- TAP (Transcript Assembly Program) and TIP (Transcript Isoform Prediction) WUSTL (USA)
- TFBIND (searching transcription factor binding sites) RIKEN (Japan)
- TFExplorer (integrated analysis database for predicted transcription regulatory elements) Daejeon (Korea)
- TFSCAN (scans DNA sequences for transcription factors) Pasteur (French)
- TRES (Comparative Promoter Analysis) Singapore
- tRNAscan (Search for transfer RNA genes in genomic sequence) Washington (USA), see also Pasteur, see also FAStRNA Pasteur (French)
- WWW AntiHunter (tool to detect potential EST antisense transcripts) Milan (Italy)
- Xpound Pasteur, see also advanced form (French)
- Profile of thermal denaturation
- MELTING (enthalpie, entropy and melting temperature) Pasteur (French)
- Poland Dusseldorf (Germany)
- Oligo Tm Alces (Minnesota)
- Tm server (Compute minimum folding energies and Tm) RPI (Zuker)
- Atypical sequences
- ZInfo Alces (Minnesota) : based on Markov model
- Repeats
- ACMES (fast multiple-genome searches for short repeat sequences with concurrent cross-species information retrieval) Missouri (USA)
- Dst Alces (Minnesota)
- Dot Plot Alces (Minnesota), see also 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)
- Locate human repeats (image) Alces (USA)
- MREPATT (Consecutive Multiple REpeated PATTerns) LSI (Spain)
- MREPS (finding tandem repeats) LORIA (French)
- PALINDROME (looks for inverted repeats in a nucleotide sequence) Pasteur (France)
- REPATT LSI (Spain)
- RepeatE ITBA (Italy)
- RepeatMasker (screens DNA sequences against a library of repetitive elements) Washington (USA)
- 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)
- SIFT (predictions for what amino acid substitutions will affect protein function) FHCRC (USA)
- 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 finder DBS (USA)
- Search DNA sequences for an aminoacids pattern
- Specific sites search
- AliBaba2 (prediction of transcription factor binding sites by context dependent matrices generated from TRANSFAC) Magdeburg (Germany)
- COMET (significant clusters of motifs in a DNA sequence) ZLab (USA)
- ConSite (prediction of regulatory elements using cross-species comparison) Stockholm (Sweden)
- ELM (predicting functional sites (described by linear motifs) in eukarytic proteins) EMBL (Germany)
- Improbizer (motifs in DNA or RNA sequences that occur with improbable frequency) UCSC (USA)
- FastM and ModelInspector (distance-correlated transcription factor binding sites) GSF (Germany), see also Genomatix, see also GBF
- MatInspector, see also Genomatix : detection of consensus matches in nucleotide sequence data (transcription factor binding sites) from a large library of matrix descriptions that can be retrieved from the TRANSFAC database (Germany)
- 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)
- PatSearch (search for potential transcription factor binding sites) GSF (Germany)
- PolyA signals CSHL (USA)
- Predicting activities of functional sites in DNA/RNA MBS (Russia)
- PROMO (identification of putative transcription factor binding sites) LSI (Spain)
- RGSiteScan program (potential binding sites of 37 transcription factors) MBS (Russia)
- S_Site (searching for E2F sites) GBF (Russia)
- SEQSCAN (matrix : Sigma-54 Promoters, IhF) Penn State (USA)
- 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)
- Structure
- Bend.it (Prediction of bendability and propensity to curvature from DNA sequences) ICGEB (Italy)
- CARNAC (folding families of related RNAs) Lille (French)
- CRAFT (DNA Bending Stiffness Features) MBS (Russia)
- Curve.it (Prediction of DNA curvature from static geometry models) ICGEB (Italy)
- EFN : Energy determinization (DNA, RNA) (Zuker)
- DNA Folding (Zuker) RPI, mirror at MBC (Australia), mirror at Bielefeld (Germany)
- ERPIN (tool to profile-based RNA motif identification) Marseille (French)
- Mfold : RNA Folding (Zuker), mirror at MBC (Australia), mirror at Bielefeld (Germany)
- GPRM (finding common secondary structure elements) Chiao Tung (Taiwan)
- ILM (predicting RNA secondary structures with pseudoknots) Washington (USA)
- Model.it (3D model of DNA molecule) ICGEB (Italy)
- 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)
- 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)
- 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)
- RNASoft (PairFold, CombFold, RNA Designer) Columbia (Canada)
- Sfold (Sirna, Soligo, Sribo, Srna) New York (USA), another link
- SSU (rRNA Secondary Structure Prediction and Alignment) UCSC (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
- BLOCKS
- BLIMPS (BLocks IMProved Searcher) Pasteur (France)
- BLOCKS WWW Server FHCCRC (search and construction) (Hutchinson)
- IMPALA (Search BLOCKS) FHCRC (USA)
- Identification of protein family
- 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), see also 3matrix
- Family Pairwise Search SDSC (USA)
- FAN (fingerprint analysis of nucleotide sequences) Manchester (UK)
- GeneFIND Family Identification System PIR (USA)
- GIST-SVM (mismatch string kernels for discriminative protein classification) Columbia (USA)
- Identify (from the BLOCKS and PRINTS databases) Stanford (USA)
- iMOT (for identifying conserved spatially interacting regions across proteins) Uttar Pradesh (India)
- MASIA (based on identification of short conserved sequence motifs common to a protein family or superfamily) Texas (USA)
- MitoPred (a genome-scale method for predicting mitochondrial proteins) San Diego (USA)
- MOTIF (Prosite, Blocks, Prodom, Prints, Pfam) Kyoto (Japan)
- PeCoP (automatic determination of persistently conserved positions in protein families) Bioinformatics (USA)
- Picasso (generating a covering set of protein family profiles) EMBL-EBI (UK)
- 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), another link
- PSCAN (scans proteins using PRINTS) Pasteur (France), see also UMMS (USA)
- P-val FingerPRINTScan Manchester (UK)
- Search the PRINTS & PROSITE Database Leeds (UK)
- SVMMER (classification and characterization of proteins) ANL (USA)
- Motifs
- Consensus (identification of consensus patterns in unaligned DNA and protein sequences) Pasteur (France)
- 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)
- 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 Pasteur (France), see also EBI, see also InfoBioGen (France), see also Expasy
- PRED-GPCR (GPCR recognition and family classification server) Athens (Greece)
- Scan_for_matches Pasteur (France)
- 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)
- ProfileScan ISREC : Search a library of profiles with your sequence, see also ISREC
- 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) MRC
- Analysis tools package
- BCM Search Launcher BCM (USA)
- HNB (Family, function, structure) Berlin (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)
- PROSPECT-PSPP (an automatic computational pipeline for protein structure prediction) Georgia (USA)
- Analyze
- AA Composition, MW, OD, pI, titration curve ABIM (in french)
- AA Composition SBDS (UK), see also BMB
- pI et Mw Expasy
- ASAP (Analysis of Sequence and Aminoacid Probabilities) Rockefeller (USA)
- ASC IMP (Analysis of protein surface : Van-der-Waals, energy, Hydrophilicity, Hydrophobicity)
- CAST (Compositional Bias Detection Algorithm) EBI (UK)
- ConSeq (identification of functionally and structurally important residues) Tel Aviv (Israel)
- CUTTER (generate peptide fragments by the enzymatic or chemical cleavage) Tours (France)
- CysPred (predicting the redox state of Cys residues from sequences or multiple sequence alignments) Rockfeller (USA), see also another link, see also CIRB
- Cysteines Bonding State and Connectivity Predictor Firenze (Italy)
- 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)
- Hydropathy Plot Penn State (USA)
- Hydrophilicity/Hydrophobicity Search and Comparison Server Weizmann (Israel)
- Molecular weight MCC (UK)
- 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 (France)
- PEST Sequence Utility (Proteins with intracellular half-lives of less than two hours are found to contain regions rich in P,E,S,T) LRIT (UK), see also EMBnet (Austria)
- PFMUTS (analyzes possible single and double mutations of a peptide fragment, given its mass and a closely related sequence) Wellington (New-Zealand)
- 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 (France)
- Profiles BMB (Eisenberg, Kyte, Transmembrane, Accessibility, Flexibility, GOR)
- Profiles (Hopp, Kyte, Karplus, Parker, Argos) PBIL (France)
- 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
- 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
- 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
- Anagram (protein function assignment) Malaga (Spain)
- Cleavage Site Prediction Server Berlin (Germany)
- 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)
- iPSORT (site predictor for N-terminal sorting signals) Tokyo (Japan)
- LOCnet and LOCtarget (sub-cellular localization for structural genomics targets) Columbia (USA)
- Predicting Subcellular Localization of Proteins using Machine-Learned Classifiers Alberta (Canada)
- PrediSi (prediction of signal peptides and their cleavage positions) Braunschweig (Germany)
- PSORT 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)
- SIGFIND (Signal Peptide Prediction) Heraklion (Greece)
- Prediction of secondary structure
- AGADIR EMBL (Germany) : predict the helical content of peptides
- AllAll ETH Zurich (surface peptide, break)
- BetaTPred (Prediction of ß-turns in proteins using statistical algorithms) Chandigarh (India)
- Beta-turn types I, II, IV and VIII prediction (neural network) Chandigarh (India)
- Biocomputing Tools (FT, SecStr, Pred-TMR, Pred-TMR2, OrienTM, CoPreTHI, Pred-Class, LSQR, SCAR) Athens (Greece)
- Coiled-coil prediction PBIL (France), see also Texas (USA)
- COILS : Prediction of Coiled Coil Regions in Proteins EMBNet
- Consensus secondary structure prediction PBIL (France)
- 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)
- 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)
- GOR Secondary Structure (Garnier, Osgoodthorpe and Robson) SBDS (UK), see also BMB
- GOR4 (J. Garnier, J.-F. Gibrat, B. Robson) ABS (DCRT-NIH)
- GOR I, II, IV PBIL (France)
- 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)
- Jpred (A consensus method for protein secondary structure prediction) EBI (UK)
- K2d (Prediction from CD spectrum) UGR (Spain)
- LearnCoil-Histidine Kinase Scoring MIT (USA)
- LearnCoil-VMF (coiled-coil-like regions in viral membrane-fusion proteins) MIT (USA)
- 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 (San Francisco) info for service by mail
- 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), another link
- PDisorder Softberry (USA)
- PEPCOIL Pasteur (France)
- PEPWHEEL Pasteur (France)
- PHD PBIL (France)
- Predicting the structure of your sequence via 123D threading GMD-SCAI (Germany), see also NCI (USA), see also Sanger (UK)
- PredictProtein (MaxHom, EvalSec, PHDSec, PHDacc, PHDhtm, PHDTopits EMBL (Germany), see also Cubic (USA), see also CMBI (Netherlands)
- PREDATOR Pasteur, see also PBIL
- Prof (Multiple alignment and structure prediction)) Wales (UK)
- Protein Sequence Analysis (SSP, NNSSP, SSPAL) Sanger (UK), see also SoftBerry (USA)
- 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)
- SDSC (Protein Structure Homology Modeling Server) San Diego (USA)
- Secondary Structure Prediction (Coils, nnpredict, PSSP) BCM
- SECOST (sequence-conformation-structure database for amino acid residues in proteins) Nebraska (USA)
- Simpa96 (optionally multiple prediction with an alignment) PIBL, see also ABS-NIH (USA)
- 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)
- 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)
- SSP ou NNSSP (BCM Launcher) BCM (USA)
- SSPRED NYU, see also SstructurePred
- SSPRO (secondary structure prediction based on Bidirectional Recurrent Neural Networks) California (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
- Bipartite NLS Locator Cambridge, (A bipartite NLS is defined by a pair of basic amino acids, separated by a spacer of 10 amino acids from a cluster of five amino acids (of which at least three must be basic))
- DBS-PRED (predictions of DNA-binding proteins and binding sites) New Delhi (India)
- PredictNLS (analysis and determination of Nuclear Localization Signals) Columbia (USA)
- NRSAS (nuclear receptor structure analysis) Nijmegen (The Netherlands)
- SubLoc (protein subcellular localization : cytoplasmic, extracellular, mitochondrial and nuclear) Tsinghua (China)
- Specific sites
- Anagram (protein function assignment) Malaga (Spain)
- ANTIGENIC (finds antigenic sites in proteins) Pasteur (France)
- Antigen Selection Pressure on Immunoglobulin Genes Stanford (USA)
- ChloroP (identification of chloroplast transit peptides and their cleavage sites) CBS (Denmark)
- DBS-PRED (predictions of DNA-binding proteins and binding sites) New Delhi (India)
- FindMod (potential protein post-translational modifications and potential single amino acid substitutions) Expasy (Switzerland), see also FindPept
- GPI Predictor (locating potential GPI-modification sites) IMP (Austria)
- HLA Peptide Binding Predictions NIH
- HLA-DR4Pred (prediction of peptides binding with MHC class II allele HLA-DRB1*0401) Chandigarh (India), mirror at Bioinformatics
- 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)
- MHCPred (prediction for epitopes bind to MHC class I molecules) Compton (UK)
- Myristoylator (predicts N-terminal myristoylation of proteins by neural networks) Expasy (Switzerland)
- NetAcet (prediction of N-terminal acetylation sites) CBS (Denmark)
- NetChop (predictions for cleavage sites of the human proteasome) CBS (Denmark)
- NetPhos (Protein Phosphorylation Prediction) CBS (Denmark)
- NetPicoRNA (Posttranslational cleavage by picornaviral proteases) CBS (Denmark)
- NickPred (prediction of proteolytic sites in a protein structure from the PDB) Manchester (UK)
- PLOC (prediction of protein subcellular locations) Kyoto (Japan)
- 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) INRA (French)
- PREDEP (MHC Class I epitope prediction) Jerusalem (Israel)
- PredPhospho (predicts phosphorylation sites of protein sequences) Seoul (Korea)
- 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)
- RASPODOM (rapid motif-based prediction of circular permutations in multi-domain proteins) Munster (Germany)
- SIGCLEAVE (signal cleavage sites) Pasteur (France), see also UMMS (USA)
- Sulfinator (predicts tyrosine sulfation sites) Expasy (Switzerland)
- SVMHC (prediction tool for MHC I binding) Stockolm (Sweden)
- TargetP (predicts the subcellular location of eukaryotic protein sequences) CBS (Denmark)
- TargId (search for target proteins for pharmaceutical applications) GMD (Germany)
- TRANSCOUT (detection and evaluation of conserved motifs in prokaryotic and eukaryotic sequences of proteins with a gene regulatory function) Barcelona (Spain)
- ZZIP (Leucine Zipper Prediction) TBI (Germany)
- 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 (USA)
- HMMTOP Budapest (Hungarian)
- kPROT Weizman (Israel)
- PHAT (Sequence Comparison for Transmembrane Sequences) FHCRC (USA)
- PHDhtm (transmembrane helix prediction) PBIL (French)
- PRED-TMBB (predicts the topology of ß-barrel outer membrane proteins) Athens (Greece)
- PredTmr (predicts transmembrane segment in proteins) Athens (Greece)
- 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)
- TMDET (detection of transmembrane regions by using 3D structure of proteins) Budapest (Hungary)
- TMHMM (CBS) V2.0 (Denmark)
- TMPred ISREC (prediction of membrane-spanning regions and their orientation by statistical analysis of TMbase)
- TMSTAT (Statistical analysis of transmembrane sequences) Yale (USA)
- TopPred 2 (orientation and location of transmembrane helixes) Pasteur
- TSEG (Prediction Tool for Transmembrane SEGment in Proteins) Kyoto (Japan)
- SOSUI TUAT (Japan)
- Structure 3D
- 3DALIGN Tokyo (Japan)
- 3D-JIGSAW (builds three-dimensional models for proteins based on homologues of known structure) BMM (UK)
- 3D-PSSM (Protein Fold Recognition (former Foldfit)) BMM (UK)
- 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) San Diego (USA)
- 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)
- CSR (Maximal Common 3D Substructure Searching) Pasteur (France)
- DALI Server EBI (UK)
- 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)
- Environ (accessible as well and buried surface area) Pasteur (France)
- ESyPred3D Namur (Belgium)
- FATCAT (for flexible structure comparison and structure similarity searching) La Jolla (USA)
- Fold prediction 3D (based on homologous sequence search) EMBL (Germany)
- 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)
- HBPRINT (Detection of hydrogen-bond signature patterns in protein families) Bangalore (India)
- 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)
- 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)
- MONSTER (inferring non-covalent interactions in macromolecular structures) Northwestern (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)
- Pairwise Superposition of Protein 3D Structures CIGB (Cuba)
- PDB2PQR (an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations) Washington (USA)
- PDBSiteScan (searching for active, binding and posttranslational modification sites in the 3D structures of proteins) Novosibirsk (Russia)
- PINTS (patterns in non-homologous tertiary structures) EMBL (Germany)
- PoPMuSiC (rationally designing point mutations in protein structures) Bruxelles (Belgium)
- ProteinDBS (a real-time retrieval system for protein structure comparison) Missouri (USA)
- ProteMiner-SSM (search for structural motifs) Taipei (Taiwan)
- Qgrid (clustering tool for detecting charged and hydrophobic regions in proteins) Iizuka (Japan)
- RPFOLD Chandigarh (India)
- Sausage ANU (Australia)
- 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), see also Sanger
- 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 (France)
- Site-Scan (binding site) Stanford (USA)
- 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)
- Swiss-Model Expasy (An Automated Knowledge-based Protein Modelling based on Blast, Fasta, Sim, CompAli, ProMod and CHARMm)
- Swiss-Model 7TM Interface Expasy (Switzerland)
- TOP (compare two Protein structures : fil in PDB format) Stockholm (Sweden)
- TUNE (Threading Using Neural nEtwork) : the measure of protein sequence-structure compatibility MRC (UK)
- VAST (Vector Alignment Search Tool) NCBI (USA)
- Alignments
- ALIGN (alignment of 2 sequences : fasta) IGHM (France)
- Align Two Polypeptide Chains by Combinatorial Extension SDSC (USA)
- Align two sequences SBDS (UK)
- Align two sequences USC (USA)
- Alignment Comparison UCSC (USA), see also tuneup, 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)
- AllAll ETH (Switzerland)
- AltAVisT (Alternative Alignment Visualization Tool) Bielefeld (Germany)
- AMAS (read an alignment to enhance conserved aminoacids) Barton group (UK)
- AVID (align two sequences) Berkeley (USA), another link
- Bellerophon (detects chimeric sequences in multiple sequence alignments) Brisbane (Australia)
- Blast 2 sequences (alignment using blast) NCBI, see also UMMS, see also Pasteur, see also Toulouse
- BLock Gap Sizes (calculates inter-block gap sizes for blocks in a CLUSTAL multiple alignment) EMBL (Germany)
- Clustalw
- Clustalw 1.6
- Clustalw 1.7
- Clustalw 1.8
- ComAlign: Combining many multiple alignments in one improved alignment Pasteur (France)
- Consensus (calculates the consensus for the CLUSTAL or MSF multiple alignment) EMBL (Germany)
- Consensus (alignment for reliable framework prediction in homology modeling) Boston (USA)
- COSA (clustal ouput structural analysis (T. Rose)) Pasteur (French)
- CRASP (Correlation Analysis of Sequences of Proteins) MBS (Russia)
- DBA (Dna Block Aligner) Sanger (UK)
- DbClustal (Align your Protein to the Blast Top Sequences found in SPtrEMBL) Strasbourg (French)
- DCA (Divide-and-Conquer Multiple Sequence Alignment Bielefeld (Germany)
- DDS2 (efficient combination of multiple word models for improved sequence comparison (2)) Iowa (USA)
- DIALIGN Bielefeld (Germany), see also GSF (Germany), see also Pasteur (France)
- DRUID (localization of recombination breakpoints in an alignment of sequences) Pasteur (French)
- DSC (Multiple alignment and structure prediction) ICRF (UK)
- EST2GENOME (align EST and genomic DNA sequences) Pasteur (France)
- ESTScan EMBNet, see V2
- Filtersites (Filter conserved sites in an alignment) Pasteur (French)
- 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)
- ITERALIGNv1.1 (multiple alignment of protein sequences) Stanford (USA)
- K2 (protein structure alignment program) ZLab (USA)
- 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)
- LASSAP (LArge Scale Sequence compArison Package) Pasteur (France)
- LFasta (Local Alignment Tool for Nucleic Sequences) ACNUC (France)
- LGA (method for finding 3D similarities in protein structures) LLNL (USA)
- MAP2 (multiple alignment of syntenic genomic sequences) Iowa (USA)
- MASIA (recognition of common patterns and properties in multiple aligned protein sequences) Texas (USA)
- 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 (multiple alignment) Berkeley (USA)
- MBS Aligner MBS (USA)
- MGAlignIt (align mRNA sequences to genomic sequences) Singapore
- MSA (Ctree, MSA, Clustal) Michigan (USA)
- MULALBLA (Multiple alignment with Blast) U-ParisSud (French)
- MultAlign (Options : Score, GapAdjust, ProbModel, RootedTree, MSA ..) ETHZ (Switzerland)
- Multalin PBIL (France)
- Multalin LGC (French)
- Multalin Toulouse (French)
- Multiple alignement (GeneBee) Moscou
- Multiple Sequence Alignment (MAP) Michigan (USA)
- Multiple Sequence Alignment NYU (USA)
- Multiple Sequence Alignments (Clustalw1.7, 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
- NEEDLE (Needleman-Wunsch global alignment) Pasteur (France)
- Pair-wise and multiple alignment of genomic sequences using CHAOS and DIALIGN Gottingen (Germany)
- Pairwise Global Alignment NYU (USA)
- 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)
- 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
- POA (Multiple Sequence Alignment Using Partial Order Graphs) UCLA (USA)
- Praline (Multiple Sequence Alignment with many options) Amsterdam (The Netherlands)
- PRSS (evaluate the significance of a protein or DNA sequence similarity score) EMBNet
- RevTrans (constructing alignments of coding DNA from aligned amino acid sequences) CBS (Denmark)
- SAM UCSC ( linear hidden Markov model), documentation, see also Pasteur
- 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)
- Spidey (mRNA-to-genomic alignment program) NCBI (USA), another link
- 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)
- 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 CMBI, see also IGS
- ToPLign (standard pairwise and multiple alignment methods) GMD (Germany)
- VerAlign (multiple sequence alignment comparison) Amsterdam (The Netherlands)
- 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) LORIA (French)
- ZPRED LICR (MultPredict Secondary Structure of Multiply Aligned Protein Sequences : format de l'alignement AMPS)
- 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)
- CVTree (a phylogenetic tree reconstruction tool based on whole genomes) Beijing (China)
- FastDNAml Pasteur, see also advanced form, see also InfoBioGen
- FootPrinter (designed for phylogenetic footprinting) Washington (USA)
- Gblocks (eliminates poorly aligned positions and divergent regions of a DNA or protein alignment for phylogenetic analysis) EMBL (Germany)
- LVB (Reconstructing Evolution With Parsimony And Simulated Annealing) Pasteur (French)
- Molphy (ProtML, NucML, ProtST, NJDist) Pasteur (France)
- PhyloBLAST (facilitating phylogenetic analysis of BLAST results) Vancouver (Canada)
- Phyloblock (align sequences and build a tree) ANL (USA)
- Phylodendron (phylogenetic tree printer) IUBIO (USA)
- Phyloquart (parciquart, distquart, qstar, addquart) Pasteur (France)
- Phylogenetic tree prediction (from an alignment) Moscow
- Phylogenetic Web Profiler GSF (Germany)
- PHYLIP
- Bari
- BRUS
- CBiB
- CBR-RBC
- Indiana
- Oxford (consense, dnadist, dnapars, fitch, kitsch, neighbor, protdist, protpars)
- Pasteur (sequence data, distance matrix, trees, discrete state, boostrap)
- Principal Coordinates Analysis Lyon (French)
- Puzzle (Tree reconstruction for sequences by quartet puzzling and maximum likelihood) Pasteur, advanced form (French), see also kun
- 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)
- SeqGen (Simulation of DNA sequence evolution) Pasteur (France)
- Shadower (generalized hidden Markov phylogeny) Berkeley (USA)
- 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)
- Supertree (algorithms for ancestral divergence dates and nested taxa) Christchurch (New-Zealand)
- The Transformation Distance (A dissimilarity measure based on large mutations) Lille (France)
- Weighbor (Weighted neighbor joining) Pasteur (France)
Others
- Genetic
- FunMap (functional mapping of complex traits) Florida (USA)
- HAP (haplotype reconstruction from genotype data using imperfect phylogeny) Berkeley (USA)
- HaploBlockFinder Cincinnati (USA)
- IMpRH Web Server INRA
- LIAN (tests the null hypothesis of linkage equilibrium for multilocus data) Max-Planck (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)
- QGE gSCAN Hutchinson (USA)
- ABS (QL prediction, MUSEQAL, Clustal, GOR4, FoReSST) NIH (USA)
- Alignment Tools (Simmat, Malgen, Malig, Lova) LSI (Spain)
- Automated analysis
- All-IN-ONE SEQ-ANALYZER (Homology Search, Protein Analysis, DNA Analysis) Michigan (USA)
- ASTRAL (Compendium for Sequence and Structure Analysis) Stanford (USA)
- Barton Group WWW Server (Amas, Scanps, Amps, Assp, Jpred, ProEST, 3Dee) 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 Phylogenomics (Protein structure, function, Evolutionary Tree, Homology Model, Multiple alignment ..) Berkeley (USA)
- BiBiServ Sequence Analysis Department Bielefeld (DCA, GeneFisher, RIFLE, ROSE, Splits tree, ..) (Germany)
- BioInfo3D (C-alpha, FlexProt, MultiProt, Mass, PatchDock, SiteEngine) Tel Aviv (Israel)
- Bioinformatics Center (PredictProtein, Meta, PredictNLS, Eva, DSSCont, NORSp) Columbia (USA)
- Bioinformatics research center (Animators, CombAt, distanceP, Foldalign, Hudson, MatrixPlot, RecPars, Rateshift, RNA folding, SLASH, tmRDB ...) Aarhus (Denmark)
- Bioinformatics resources (DigiNorthern, KaryoReader, DNA helical stability) Buffalo (USA)
- Biocomputing Tools (FT, SecStr, Pred-TMR, Pred-TMR2, OrienTM, CoPreTHI, Pred-Class, LSQR, SCAR) Athens (Greece)
- BioInformatics & Molecular Analysis Section BIMAS (HLA Binding Prediction, Promoter Scan, Signal Scan, GCG-Lite)
- Bioinformatics and Pattern Discovery IBM (Pattern Discovery, Multiple Sequence Alignment, Homology Search) (USA)
- BioInformatics ressources UMMS (Restriction, TFScan, ORF, Primer, Signal sequence cleavage, Garnier, PRINTS, Blast)
- Bioinformatics Services at IFOM (Blast, HMMER, GenScan, Assembly, EST Machine, SMS, SeWeR, JaMBW) Rome (Italia)
- Bioinformatics Toolkit (Blast, Fasta, Clustalw, PredictProtein, SEWER interface) CMBI (The Netherlands)
- Bioinformatics Tools (Praline, VerAlign, Alicao, 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, Phylip ...) Hong Kong
- Bioinformatics Web (Protein and DNA analysis, EMBOSS, Phylogeny) Indiana (USA)
- BioI@Sista (Maran, AQBC, Intergenic select, MotifSampler, MotifScanner, Go4G, Toucan) Leuven (Belgium)
- Biological computing (Sequence analysis, Genomics, Proteomics) Weizmann (Israel)
- Biological programs accessible through the Web server of Pasteur (France)
- Biomolecular Modelling Laboratory (Sawted, 3D-PSSM, Prof, Domains, 3D-JIGSAW, Domain Fishing) BMM (UK)
- BioWWW (Codontree, Patscan, UTRscan, Wordup, Markov) Bari (Italy)
- BLASTULA (the server of Blast servers) GIFTS (France)
- The Brutlag Bioinformatics group (emotif, identify, scan, decypher, alion) Stanford (USA)
- Calculations (Sequence utilities, Trnaslation, rare codons, PCR, Spectro, Bacteria growth, ..) at MolBiol (Russia)
- CBC protein analysis (PANAL) CBC (Prosite, Blocks, Prints, Pfam) (USA)
- Comparative genomics (ECR browser, rVista, Creme, Genome alignment, Mulan, zPicture, eShadow) LLNL (USA)
- Computational Biochemistry Research Tools ETH (Darwin, AllAll, AllAllDB, MassSearch, MultAlign, NuclPepSearch, PepPepSearch, TreeGen)
- Computational Biology IBM Research (USA)
- Computational Biosciences Tools (GenQuest, Grail, PROSPECT, Pipeline, Domain Parser, Mira) Oak Ridge (USA), another link
- Computational Services developed and offered by EMBL (Germany), another link
- Computer Programs (RGSites scan, Predicting activities of functional sites in DNA/RNA, CRASP, CRAFT) MBS (Russia)
- CSE on line software (EULER, GRIMM, MGR) UCSD (USA)
- DDBJ Search and analysis (Blast, Fasta, Ssearch, Clustalw, Libra) DDBJ (Japan)
- DeCypher server (Blast, ClustalW, Framesearch, HMM Framesearch, HMM, Profile, Smith-Waterman) Stanford (USA)
- Dragon Genome Explorer (Promoter finder, CG+ PF, ATG finder, CpGIslands, Splice sites, PolyA) BRUS
- Easy (Blast, Fasta, Pfam, Prints, Prosite, Profiles, Blocks) Manchester (UK)
- EBI services EBI (Database, Query, Similarity ...), other services EBI (Dali, Bic, Bic_SW, Blast, Fasta3, Clustalw, GeneMark, Ppsearch, Prat, Restrict, SAPS), emboss tools
- Computational Genomics Group CGG-EBI
- Elephant Cluster (Blst, Clustal, SMS, Emboss, Fasta ..) Singapore
- Expasy tools menu , see also Swiss-Model: Automated Protein Modelling Server
- Expression Profiler EBI (UK)
- Fasta Programs (Fasta, Lalign, Plalign, PRSS, Hydrppathy, Garnier) Virginia (USA)
- Free on line access (ElDorado, Chip2Promoter, PromoterInspector, MatInspector, SMARTest, DiAlign) Genomatix
- FUGE (Ka/Ks, RegExpMaker, Pratt, BOMP, XHM) UiB-UiO-NTNU (Norway)
- Galaxie (Blast, Align, HMM : sequence identification through automated phylogenetic analysis) Goteborg (Sweden)
- GeneBee services Moscou
- Genestream (Blast, Fasta, Align, LFasta, LAlign, SSearch, Map ...), IGHM, see also IGHM (France)
- Genetics Programs (Transmit, Phase, Phamily, Haploxt, Genoform, Haploform) Oxford (UK)
- Genomic analysis Web Tools Sanger (UK)
- Helmholtz Network for Bioinformatics (Protein analysis, families, function, structure ...) HNB (Germany)
- HIV Sequence Database tools LANL (USA)
- HMM Applications (Compare, Query, Tune Up : hidden Markov model) UCSC (USA)
- HNB (Family, function, structure) Berlin (Germany)
- Honig Lab's Software Server (DelPhi, Surfv, Decoy, Side Chain, Loop, Structure Alignment,..) Columbia (USA)
- IBM Bioinformatics Groups (Protein annotation, MSA, Pattern discovery, Gene identification...) IBM
- In silico analysis of complete bacterial genomes (PCR, AFLP-PCR and endonuclease restriction) Vitoria-Gasteiz (Spain)
- Integrated Analysis Services (with registration) HGMP (BLAST, NIX, GLUE, PIE, RHyME, MAGI)
- Intronerator (collection of tools for exploring the molecular biology and genomics of C. elegans) California (USA)
- ISREC Software Homepage (Lausanne) ISREC (BOXSHADE 3.0, Coils, EPFL-BLAST, PatternFind, ProfileScan, PrositeScan, SAPS, TMPred)
- ISU server (AAT, GeneSequer, SplicePredictor, MyGV, Diverge, MuSeq Box, Alignment,..) Iowa (USA)
- Jade development environment and demos Montpellier (France)
- Java-based Molecular Biology Work Bench Toldo (Alignment Editor, Pattern Searching, PCR, pI, Oligo, Map, Translate, ..), see also BBS (Australia)
- LBNL Human Genome Informatics Group LBNL (Gene, promoter, splice sites prediction : (HMM and NN methods))
- Logiciels au LCB (ESTA, FSED, Recsta) LCB (French)
- Logiciels pour la biologie (Blast, Clustalw, HMMER, Phylip, Emboss Package, IPPRE, Clustering) CBiB (French)
- Mass Spectrometry Facility UCSF (MS-Fit, Tag, Edman, Digest, Product, Comp), see also ProteinProspector
- META PredictProtein server (SignalP, NetOglyc, NetPicoRNA, ChloroP, JPred, TmHMM, ToPred, DAS, FRSVR, SAMT98, Swiss-Model, CPHmodels) Columbia (USA)
- Meta-Server (Pcons2, 3DSHOT3, Blast PDB-Blast, ORFeus, FFAS, 3D-PSSM, GenTHREADER, mGenTHREADER, INBGU, Sam-T99, FUGUE, 123D+, SUPERFAMILY) BLBII (Poland)
- MMTSB (Multiscale Modeling Tools in Structural Biology) SRI (USA)
- Modelling server (Vriend's Group : WHAT_IF, DSSP, Check, Secondary structure...) CMBI, see also WHAT IF Web interface
- 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
- NCSA BIOLOGY WORKBENCH NCSA (Database Search, Blast, MSA)
- NETASA (Prediction/ analysis tools : Qgrid, TMBeta, RVP-Net, ASA view, DBS-Pred, Netasa) Iizuka (Japan)
- NetMul PBIL (online multivariate analysis system)
- NIMR Tools (Quest, Humanisation, Mview, Praline, Repro, Tune1D, Pops, Sap, Psap) NIMR (UK)
- NPS@ (Network Protein Sequence @nalysis) PBIL (France)
- On-line Resources From UMBER (Align, Bioactivity, Cinema, Easy, FingerPRINTScan, PRINTS) Manchester (UK)
- Online Services of the Institute of Enzymology (Hmmtop, Scpred, Scide, Das-Tmfilter, CysRedox, Das) Budapest (Hungaria)
- The Open-Acces Institute (SMS 2: Sequence Manipulation, SeWeR: Sequence Analysis, Savvy: Plasmid Map Drawing, PrimerX: Mutagenic Primers ...) Bioinformatics
- PAPIA (Protein structure similarity, Homology, Alignment, TFSEARCH) RWCP (Japan)
- PIR Integrated Environment for Sequence Analysis (IESA) Georgetown (USA)
- PIR Searching Databases (Blast, Pattern, Alignment, GeneFind) Georgetown (USA)
- Plant databases and tools (Motif Sampler, Cluster analysis, SPADS) Plant systems Biology (Belgium)
- Prediction servers (CPHmodels, HMMgene, NetGene, NetOglyc, NetPicoRNA, NetPlantGene, NetStart, SignalP) CBS (Denmark)
- Predictor (B2tmpred, Cornet, Cyspred, Dcon, Irene, MaxSubSeq, Ispred, Rcnpred, Secpred, Spep) Bologna (Italy)
- PRODRG (Vriend's Group : a small molecule interpretation system ; GROMOS, WHATIF, MOL2, MOLDES) Dundee (UK) (PDB format)
- Programs for Comparison and Recognition of Protein Structures (123D, SARF2, PDP) NCI-FCRDC (USA)
- Protein Folding and Design Group (Agadir, CHEY, SH3, ADA2h, Helical, Beta) Heidelberg (Allemagne)
- Protein Prospector (MS-Fit, MS-Tag, MS-Seq, MS-Pattern, MS-Digest, MS-Product, etc.) UCSF (USA), see also Melbourne (Australia)
- Protein Structural Analysis (Secondary structure, Folding, PimaII, Threading) BMERC (USA)
- Protein Structure Prediction (Casp1, Casp2, Casp3, SOV, ACE) LLNL (USA), see also ProtInfo
- PROWL Rockfeller (MassBank, MassRef, Protein identification ..), see also ressources
- PSCAN (Aligning 2 sequences, finding a match in the database) Stockholm (Sweden), see also services
- PSIPred server (PSIPred, MEMSAT, GenTHREADER) London (UK)
- Public WWW services (EMBOSS, PHD, Prosite, Phylip, Clustalw, Phylodendron, HTH,..) EMBNet (Spain)
- RDP-II Online Analyses (Probe, Align, Distance, Chimera, T-RFLP, SubTrees..) CME (USA)
- SAGE (Serial Analysis of Gene Expression) NCBI, see also Sagenet
- Samuel Karlin Group Web Server (SplicePredictor, ITERALIGN, SSPA, GENSCAN) Stanford (USA)
- SBNet (Structural Biology Network : BioSEL, ProSAL, HetSEL) Uppsala (Sweden)
- 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)
- 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, PFScan, Coils, TmPred, Saps, ...) at EMBNet
- Services (Pattern, LFasta, LAlign, Align, Fasta, Blast, Blast2, Clustalw, Traduction) InfoBioGen in french (France)
- Services at the BUM (TFC, UTR, CDS finder, Contig, Clustalw, Fpat, LWA, SENSEI) Michigan (USA)
- Services (Gene finder, Genome search, Promoter, Protein structure, Protein location) at Softberry (USA)
- Services at TOFU (Blast, ScorePeptides, ReadSeq, FmtSeq, Coils2, SeqSearch, Primer3, ClustalW, BoxShade) Texas (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 EMBnet Norway
- Software at EMBnet ch.EMBnet
- Software at the Roth Lab (GoFish, ClusterJudge, Pnet, ChIPper, FuncAssociate) Harvard (USA)
- Structural Bioinformatics Group (Pints, InterPreTS, Proust, Coiled-coil) EMBL (Germany)
- Structural Biology on line (Fugue, TraceSuite II, Coda, Petra, Joy, Comparer) Cambridge (UK)
- Structure Prediction sever (Crystal, Fold, Moment, Errat, Verify3D, Alignment, ..) UCLA-DOE (USA)
- SWBIC (Pcappss, Blast filter, GraphAlign, Transform, SeqCheck, SeqMake, EnVirusSat) NMSU (USA)
- TBI services (ZZIP, Blast, Fasta, PRIDE, SYSTERS Cluster...) DKFZ (Germany)
- TigemNet Sequence Utilities (Blast, UniBlast, EST assembly, CAP, CompBlast, CompFasta, DPS) TigemNet (Italie)
- Tools for data mining (Blast, COGs, LocusLink, UniGene, ORF finder, Electronic PCR, VAST, CCAP, VecScreen) NCBI (USA)
- Tools Online (SIMP - Tools for SNPs data collection, integration, selection and preparation for association study on complex diseases, MutScreener - to design PCR) Chicago (USA)
- TOPS (Protein Topology : search, compare, cartoon..) EBI (UK)
- TRADAT (TRAnscription Databases and Analysis Tools) MI (Italy)
- TRANSFAC (Blast, MatInspector, FastM, PatSearch, SaGa, S-comp, Clustalw, Boxshade, FunSiteP) GBF (Germany)
- USC Computational Biology USC (Alignment, Chimera, Gene Recognition, Procrustes)
- USF WWW services (SPASM, DEJAVU, HIC-Up, MOLEMAN, MAPMAN, EDS) Uppsala (Sweden)
- Virtual Genome Center (Alces) VGC (Coding region, Dotplots, Dst, Oligo Tm, Primer, Zinfo)
- VISTA (suite of programs and databases for comparative analysis of genomic sequences) Berkeley (USA)
- Web-based analysis (Primer, Promoter Scan, Lalign, Pscan, PatmatMotif, STSSearch) Oxford (UK), see also (Phylip, Emboss, Hmmer, Sam packages) WB-Analysis
- WebGene Server ITBA (Italy) (Gene prediction, Splice, Poly A, Tata Box, MSA, CpG, Repeat, EST)
- wEMBOSS IBBM (Argentina), see also PBI (Canada), see also EBI (UK), see also OUBC (UK)
- Workbench (web-based tool for biologists) SDSC (USA)
- WWW Query (COA, PCO, Recsta, Lfasta, Pattern...) Lyon (France)
- Yeast Regulatory Tools (upstream region analysis, pattern, orf, oligo, ..) ULB (Belgium), see also LCB (Mexico)
- Zhang Lab server (Gene-finding, Promoter, Poly-A, ESEfinder) CSHL (USA)
- Index
- Analysis tools Pasteur (France)
- DNASYSTEM (Sequence Analysis Site) San Diego (USA)
- The DEAMBULUM (Optimized Maze in Molecular Biology) InfoBioGen (France)
- 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)
- CHROMA (tool for generating annotated multiple sequence alignments) Oxford (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
- JOY (protein sequence-structure representation and analysis) Cambridge (UK)
- Lowercase low-complexity regions (PSEG) Virginia (USA)
- MaxBench (Sequence comparison methods evaluated) Sanger (UK)
- ModelMaker (to construct mRNA sequences from genomic data) NCBI (USA)
- MuSeqBox (Multi-query Sequence Blast output examination) ISU (USA)
- Near Optimal Sequence Display Virginia (USA)
- PlasMapper (for drawing and auto-annotating plasmid maps) Alberta (Canada)
- POLYVIEW (a flexible visualization tool for structural and functional annotations of proteins) Cincinnati (USA)
- PTree (PRINTS Tree) Manchester (UK)
- The Protein Colourer EBI (by default, colour aminoacids according to their hydrophobicity : settings change available)
- PrettyPlot MulSeqs UMMS (USA)
- Reformat sequences Wisconsin (USA)
- RHIMS (Relative Homology Index using Mathematical Summation) visualisation of Database searches Dundee (UK)
- Sequence Shuffle (shuffle the order of characters to produce a randomized sequence with the same overall composition) Arizona (USA), another link
- SHUFFLESEQ (shuffles a set of sequences maintaining composition) Pasteur (France)
- Tools for alignments Heidelberg
- VisCoSe (visualization and comparison of consensus sequences) Muenster (Germany)