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
- 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
- BCM Proteins,
nucleic
acids [D, E, R, S]
- DISC
(Japan) (results by e-mail)
- Expasy : blast at NCBI or EPFL,
[D] with extra : analyse and align all HSPs
- GenomeNet (Japan)
[D]
- IBB
(Padoue)
- IGHM
(French) [D]
- IGS
(French [E]
- Pasteur,
advanced
form [D]
Databases : NR, Month, SwissProt,
Dbest, DBSTS, GBxxx, PDB, Vector, Kabat, NRSub, Transfac ...
- Sanger
(OmniBlast : 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 Arabidopsis TAIR, see also St
Louis [D, E]
- 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) (USA)
- Search of CDD (Conserved Domain Database : rpsblast) NCBI
(USA), see also Toulouse
(French)
- Search of dbEST, NCBI's EST database CBIL
(USA)
- Search of Dictyostelium (blastn) : Tsukuba
(Japan)
- Search of Drosophila : BDGP
(Berkeley), see also EBI [E]
- Search of EST (Human, Drosophila, Mouse, EMBLEsT..) EMBL (Germany)
- Search of E. Coli : blastn Alces
(Minnesota) [D], see also Pasteur (French)
- Search of ESTHER (cholinesterase) INRA
(French)
- Search of Fugu rubripes : blastp HGMP (UK)
- Search of Haemophilus influenzae LANL (USA)
- Search of HIV IGS
(French)
- Search of HIV, Human, Mouse Database (Stanford) simple,
see also moderate
- 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 Repeat Oklahoma (USA)
- Search of Immunoglobulins NCBI (USA)
- Search of microbial genomes NCBI,
see also OU-ACGT
(USA) (TBLASTN)
- 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 Parasite (BlastN, TBlastN, TBlastX) EBI (UK)
- Search of Plasmodium Sanbi (South
Africa)
- Search of P. falciparum Sanger
(UK), see also NCBI
- Multiple Custom Databases (P.falciparum, P.vivax, P.berghei, P.
chabaudi, EST) NCBI
(USA)
- Search of Streptococcus pyogenes Oklahoma (USA)
- Search of Yeast Alces
(Minnesota) [D]
- Search of S. cerevisiae MIPS
(Germany)
- Search of S. pombe Sanger
(UK)
- Search of Y. pestis Sanger
(UK)
- Species-Specific Protein Sequence Searches BCM
(USA)
- PRINTS Blast Manchester
(UK)
- Prodom with Blast Toulouse
[D] (+ graphic
display of the domain)
- Search of SBASE8.0 Database ICGEB (Trieste)
((results by e-mail)
- Blast for RPT IBC (Analysis of
repetitive sequence in C. elegans)
- 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)
- Search of Ex-NRL-3D (SWISS-MODEL Blast) Expasy
- 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]
- Pasteur
[D]
- Toulouse
[D]
- UMMS
[E]
- Search of Arabidopsis TAIR (USA)
- Search of NRL_3D or SwissProt PBIL
(French)
- Search of Plasmodium Sanbi (South
Africa)
- SAWTED (Structure Assignment With Text Description) BMM (UK)
- 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]
- EMBNet
(Switzerland) [D]
- GSC
(USA)
- NCGR (USA)
[D]
- Pasteur,
advanced
form [D]
- 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 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 EpoDB CBIL
(USA) [D]
- Search of Leishmania major Database Sanger
(UK)
- Search of Mouse Jackson
(USA)
- Search of Parasites EBI (UK)
- Search of P. falciparum Sanger
(UK), see also Stanford
(USA)
- Search of Prokaryotes JGI (USA)
- Search of S. cerevisiae Stanford
(USA) [D, E]
- Search of S. pombe Sanger
(UK)
- Search of Salmonella typhi Sanger
(UK)
- Search of Toxoplasma EST CBIL
(USA) [D]
- Search of dbEST TigemNet
(Italy)
- Search of microbial genomes Sanger
(follow the organism link) (UK)
- Search of TIGR Unique Gene Indices TIGR
(USA)
- 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)
- Giessen Proteins,
DNA
(Germany)
- 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 GCRDb Database (G protein-Coupled Receptor) Texas
(query by e-mail)
- Search of E. Coli Pasteur (French)
- 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)
- Needleman and Wunsch
- AbCheck UCL
(Londres) 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)
- 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,
see also Paracel
(USA)
- MPsrch DISC
(Japan) (results by e-mail), see also LBNL (USA)
- MPsrch EBI (UK)
- Search DNA and Protein Databases for Sequence Similarities (a.a. query
sequence) Oslo (Norway)
- ProfileSearch (package GCG) Weizman (access by
e-mail)
- 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
- SSAHA (Sequence Search and Alignment by Hashing Algorithm)
- Wise
- Protein/genomic or Protein/cDNA Pasteur
(French)
- Protein vs genomic Sanger
(UK)
- Protein vs cDNA 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
- MassDynSearch (searching SwissProt by protein mass after C or
N-terminal digestion) ETHZ
(Switzerland)
- MassSearch (search EMBL, SWISS-PROT) ETH Zurich, see
also www
- Mowse (search OWL) DL (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 ETH (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)
- 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)
- FPAT Regular
Expression Searching Protein Databases
- GeneFIND Family Identification System UTHCT (USA), see
also PIR
(USA)
- Halfwise (compare your DNA sequence against the whole of Pfam) Sanger
(UK)
- 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)
- MOTIF Kyoto (Japan)
- Motifs in protein databases Alces (Yeast,
Worm, Human)
- 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)
- PRP
HPT (Hashed Position Tree) Pattern Recognition program, see also for long
pattern (Search PIR)
- RAMdb Citi2 (French)
- ScanProsite
tool (Expasy) : SwissProt Pattern will be written according the
syntax of Prosite
- Screening pattern or alignment Moscou
- Proteins Alces
(Minnesota) search a subset of Genbank, see also
- DAPMAIL (see pattern definition) BRU Edinburgh (query
by e-mail)
- DNA regular expression BMERC
(USA)
- 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
(Deuchtland)
- PatScan Argonne
(Proteins or Nucleic acids, selection of genomic libraries), see also BRUS
- PatSearch (primary or specialized divisions database) Bari
(Italy)
- Scan (regular expression) Stanford (USA)
- Search for Sequence Pattern (DNA, protein) LBGBP (French)
- SeqhuntII-Match :
search the Kabat database for nucleotides or amino acids pattern
- Signal Scan (search TDF and Transfac for eucaryotic signal) : BRUS, or NIH, or search
IMD NIH, see
also Tigem
- Sequence Assembly
- CAP (Contig Assembly Program Based on Sensitive Detection of Fragment
Overlaps) InfoBioGen
(French), see also TigemNet
(Italy)
- Gene Recognition and Assembly (GRAIL) ORNL (USA)
- MERGER (merge two overlapping sequences) Pasteur
(French)
- Content - Codon usage - ...
- Biopolymer calculator Yale (USA)
- Alces Codon
usage (Minnesota)
- 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)
- 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
- 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
- MSA (Mutational Spectrum Analysis) ITBA
(Italy)
- MSBAR (mutate sequence beyond all recognition) Pasteur
(French)
- Relative Synonymous Codon Usage, G+C content and Nc values BMC
(Sweden)
- Riche en ... (graphical display of content in selected bases) ABIM (in french)
- Map (restriction)
- Arabidopsis Restriction Mapper TAIR
(USA)
- Find restriction sites Texas (USA)
- TACG UCI,
see also version
2 (USA), see also Pasteur
(French), see also CMBI
- Webcutter Yale, mirror
at Sweden
- Restenzyme Budapest
(Hungary)
- RESTRICT (finds restriction enzyme cleavage sites) Pasteur
(French)
- Restriction Enzyme Analysis Indiana,
see also Geneseo
- 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)
- WWWtacg v2.38 TACG (USA)
- Yeast Genome Restriction Analysis Stanford,
see also Reverse
Restricion Mapping (USA)
- Microarray - Genomics
- Affymetrix Data Conversion UCI (USA)
- Analysis tools NCGR
(USA)
- Clustering, Motif sampler, Intergenic select Sista
(Belgium)
- DNA Microarray Analysis Tools IGB (USA)
- GAP (Genome- wide Automated Primer) UCI (USA)
- 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)
- FUZZNUC (nucleic acid pattern search) Pasteur
(French)
- GenCANS-RDP System (classification of small subunit ribosomal RNAs) UTHCT (USA)
- MEME (tool for discovering motifs in groups of sequences) San Diego, see also Pasteur
- Scan_for_matches Pasteur
(French)
- 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)
- BRUS
- Aide PCR (in french) Citi2 (French)
- 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)
- DoPrimer (Germany)
- Electronic PCR (PCR-based sequence tagged sites (STSs)) NCBI, see also NCBI
- GeneFisher Bielefeld
(Germany)
- Hyther WSU
(USA)
- ISOCHORE (plots isochores in large DNA sequences) Pasteur
(French)
- MEDUSA Karolinska
(Sweden)
- MELTING (enthalpie, entropy and melting temperature) Pasteur
(French)
- Oligo Calculator (Java script) Pittsburg, see
also Adelaide,
see also Texas
- Oligo Calculator BioInf
(USA)
- Oligonucleotide Vital Statistics Cambridge
(MW, OD, Tm, %GC)
- PCR primer selection VGC (USA)
- 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)
- Primer Pick V 3 MIT,
see also EMBNet
- Primer 3 (new interface) MIT
(USA), see also Cambridge
(UK), see also UMMS (USA)
- Primer finder Dallas (USA)
- The Primer Generator Johns
Hopkins (USA)
- Primo Pasteur
(French)
- STSSEARCH (searches a DNA database for matches with a set of STS
primers) Pasteur
(French)
- VecScreen (tool for screening a nucleotide sequence for vector) NCBI (USA)
- Web Primer (Saccharomyces) Stanford
- 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)
- ATGpr (identifies the initiation codons in cDNA sequences) HRI (Japan)
- BCM Gene Finder (exons, splicing sites, promoter, coding region) BCM,
see also Gene
Feature Searches, see also BCM-LPT
- 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)
- Core-Promoter Finder CSHL (USA)
- Correspondence Analysis Lyon (French)
- Diogenes (examines short genomic sequences for the presence of likely
protein-encoding regions) UMN (USA)
- EcoParse (mailserver for finding genes in E. coli DNA) Info (Denmark)
- ESTMAP (tries to predict introns in DNA comparing ESTs and a query
sequence) ITBA
(Italy)
- Eukaryotic Promoter Prediction by Neural Network LBNL
- FindORF IBB
(Padoue)
- FrameD (genes and frameshifts in procaryotic sequences) INRA (French)
- FramePlot NIH-NET
(Japan)
- Frameshift check (Genomic sequencing error detection tool) EBI (UK)
- FrameShift Error Detection FSED
(Marseille)
- FrameShift Error Detection EMBL (Germany)
- FunSiteP (recognition and classification of eukaryotic promoters by
searching transcription factor binding sites) GSF
(Germany)
- GeneBuilder ITBA
(Italy)
- Gene Finder (Human, Mouse, Arabidopsis, Fission Yeast) CSHL (USA)
- GeneMark EBI (UK),
see also GIT (USA)
- Gene Recognition via Spliced Alignment USC
(USA)
- Geneid MBCRR
Boston (query by e-mail), see also IMIM
- Genie (gene finder based on Hidden Markov Models) LBLN
- GenLang (tRNA, group I intron, protein gene : "Linguistic Methods") CBIL
(Pennsylvania)
- GenMark GTSAB
Georgia (query by e-mail)
- GeneSeqer (identifies potential exon/intron structure in (plant)
pre-mRNA) ZmDB (USA)
- GETORF (finds and extracts open reading frames) Pasteur
(French)
- GenScan (Identification of complete gene structures in genomic DNA) Stanford (USA), see also Pasteur
(French), see also GeniusNet
(Germany), see also MIT (USA)
- GenView (Protein-Coding Gene Prediction) ITBA
(Italy)
- GIN (Gene Identification using Neural Nets and Homology Search) Heidelberg
(Germany)
- GRAIL ORNL 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)
- Microbial gene prediction ORNL (USA)
- mRNA ORF finder WUSTL (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)
- 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)
- ORF Finding programs Base4 (USA)
- ORFGene (Gene Structure Prediction using Homologous Proteins) ITBA
(Italy)
- PLOTORF (plot potential open reading frames) Pasteur
(French)
- Plot ORFs UMMS (USA)
- PolyA signals CSHL
(USA)
- PredictGenes (predict and verify gene structure by alignment with
homologous proteins) ETHZ
(Switzerland)
- Promoter 2 (vertebrate Pol II promoters) CBS (Denmark)
- Proscan II (predicts putative eukaryotic Pol II promoter sequences) : Minnesota,
see also Proscan I : BRUS, or NIH
- Putative DNA Sequencing Errors Check EMBL-Bork
(Germany)
- Regulatory Sequence Analysis Tools UCMB-ULB
(Belgium)
- RecSta (coding region (CDS or exon) prediction program using COA) Lyon
- RNA Genie (locates RNA genes) LBL (USA)
- ROSETTA (prediction of coding exons on a target human sequence) MIT (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)
- SpliceNet (Splicing Signals Prediction using Neural Networks) ITBA
(Italy)
- SplicePredictor (identifies potential splice sites in (plant) pre-mRNA)
ZmDB
(USA)
- SpliceProximalCheck EBI
(UK)
- Splice Site Prediction by Neural Network LBNL, see also
Berkeley
- SpliceView (Splice Prediction by using Consensus Sequences) ITBA
(Italy)
- STRING (Search Tool for Recurring Instances of Neighbouring Genes) EMBL (Germany)
- SynCod (a computing system for CDS prediction based on BLASTN output) ITBA
(Italy)
- TAP (Transcript Assembly Program) and TIP (Transcript Isoform
Prediction) WUSTL (USA)
- TFSCAN (scans DNA sequences for transcription factors) Pasteur
(French)
- tRNAscan (Search for transfer RNA genes in genomic sequence) Washington
(USA), see also Pasteur,
see also FAStRNA Pasteur
(French)
- 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)
- Atypical sequences
- ZInfo Alces
(Minnesota) : based on Markov model
- Repeats
- 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)
- PALINDROME (looks for inverted repeats in a nucleotide sequence) Pasteur
(France)
- Pythia Argonne
Illinois (query by e-mail)
- RepeatE ITBA
(Italy)
- RepeatMasker2 (screens DNA sequences against a library of repetitive
elements) Washington
(USA)
- Repeats Pasteur
(France)
- 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)
- 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)
- FastM and ModelInspector (distance-correlated transcription factor
binding sites) GSF
(Germany)
- MatInspector
: 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)
- NetStart (predictions of translation start in vertebrate and
Arabidopsis) CBS (Denmark)
- PatSearch (search for potential transcription factor binding sites) GSF
(Germany)
- Pol3scan
: searches the eukaryotic polymerase III intragenic control regions A box
and B box (Italy)
- PolyA signals CSHL
(USA)
- Predicting activities of functional sites in DNA/RNA MBS
(Russian)
- RGSiteScan program (potential binding sites of 37 transcription factors)
MBS
(Russian)
- S_Site (searching for E2F sites) GBF
(Russian)
- SEQSCAN (matrix : Sigma-54 Promoters, IhF) Penn State
(USA)
- TFSEARCH
: Searching Transcription Factor Binding Sites (Japan)
- TFScan (locates potential transcription factor binding sites) UMMS (USA)
- TESS (Transcription Element Search System) CBIL (USA)
- Transterm (database of sequence contexts about the stop and start codons
search) Otago
(New Zealand)
- Structure
- Bend.it (Prediction of bendability and propensity to curvature from DNA
sequences) ICGEB
(Italy)
- CRAFT (DNA Bending Stiffness Features) MBS (Russian)
- Curve.it (Prediction of DNA curvature from static geometry models) ICGEB
(Italy)
- EFN :
Energy determinization (DNA, RNA) (Zuker)
- Mfold
: DNA Folding (Zuker), see also RPI,
mirror at MBC (Australia),
mirror at Bielefeld
(Germany)
- Mfold
: RNA Folding (Zuker), mirror at MBC (Australia), mirror at Bielefeld
(Germany)
- Model.it (3D model of DNA molecule) ICGEB
(Italy)
- paRNAss (Prediction of Alternative RNA Secondary Structures) Bielefeld
(Germany)
- Plot.it (Plotting of general DNA parameters) ICGEB
(Italy)
- RNA Analysis (Mfold, RNAfold, eval, heat..) Pasteur
(France)
- RNA secondary structure prediction Moscou
- RNAfold Vienna
(Austria)
- RNAGA (prediction of common secondary structures of RNAs by genetic
algorithm) Pasteur
(French)
- SSU (rRNA Secondary Structure Prediction and Alignment) UCSC
(USA)
- Tinoco Plot Duesseldorf
(Germany)
- 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)
- EMatrix Stanford
(USA)
- Family Pairwise Search SDSC
(USA)
- GeneFIND Family Identification System UTHCT (USA)
- Identify (from the BLOCKS and PRINTS databases) Stanford (USA)
- MOTIF (Prosite, Blocks, Prodom, Prints, Pfam) Kyoto (Japan)
- PSCAN (scans proteins using PRINTS) Pasteur
(France), see also UMMS (USA)
- P-val FingerPRINTScan Manchester
(UK)
- Search the PRINTS & PROSITE Database Leeds
(UK)
- 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)
- 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 Helsinki,
see also InfoBioGen
(France)
- Scan_for_matches Pasteur
(France)
- SMART (Simple Modular Architecture Research Tool) EMBL (Germany)
- Prosite (search a sequence for a "prosite" pattern)
- Profile
- 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 EMBNet
- PROPHET (gapped alignment for profiles) Pasteur
(France)
- PSIC (Profile extraction from sequence alignments) Moscou (Russia)
- Repeats
- Recognition of protein sequence repeats (REPRO) MRC
- Analysis tools package
- BCM Search Launcher BCM
(USA)
- META PredictProtein server (SignalP, NetOglyc, NetPicoRNA, ChloroP,
JPred, TmHMM, ToPred, DAS, FRSVR, SAMT98, Swiss-Model, CPHmodels) Columbia
(USA)
- Network Protein Sequence @nalysis (SOPM, SOPMA, HNN, MLRC, DPM, DSC,
GOR, PHD, PREDATOR,..) PBIL
(France
- 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 EMBL
(Analysis of protein surface : Van-der-Waals, energy, Hydrophilicity,
Hydrophobicity)
- CAST (Compositional Bias Detection Algorithm) EBI (UK)
- 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)
- 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
- 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)
- Hydrophobicity (Rose, Kyte & Doolitle, Wolfenden, Janin) LANL (USA)
- Molecular weight MCC (UK)
- OBSTRUCT EMBL
(compute the largest cliques according to the structural resolution and
similarity of a protein set (PDB sequences)) : requête
- 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)
- 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)
- 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
- Volume irregularities in proteins SURVOL (PDB
format)
- Prediction of signals and site localisation
- Cleavage Site Prediction Server Berlin
(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)
- Prediction of secondary structure
- AGADIR EMBL
(Germany) : predict the helical content of peptides
- AllAll 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)
- DSC (Multiple alignment and structure prediction) Pasteur
(France)
- FoReSST (FOld REcognition from Secondary Structure prediction) NIH (USA)
- Garnier UMMS (USA)
- 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)
- 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)
- Map123d (allows to define prediction rules) Bio-lirmm
(France)
- 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
- NPS@ (Network Protein Sequence @nalysis) PBIL
(France)
- Paircoil (Predicting Coiled Coils) MIT (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),
see also BCM-LPT
- PredictProtein (MaxHom, EvalSec, PHDSec, PHDacc, PHDhtm, PHDTopits EMBL
(Germany), see also Cubic
(USA), see also CMBI
(Netherlands)
- PREDATOR EMBL
(results by e-mail), see also 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 Brunel (UK)
- Quadratic Logistic Secondary Structure Prediction without homologues,
with homologues
(ABS-DCRT-NIH)
- SDSC (Protein Structure Homology Modeling Server) San Diego (USA)
- Secondary Structure Prediction (Coils, nnpredict, PSSP) BCM
- Simpa96 (optionally multiple prediction with an alignment) EMBL, see also
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,
see also BCM-LPT
- SSPRED NYU
- SSPRO (secondary structure prediction based on Bidirectional Recurrent
Neural Networks) California
(USA)
- Nuclear regions
- Bipartite NLS Locator Cambridge, see also (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))
- SubLoc (protein subcellular localization : cytoplasmic, extracellular,
mitochondrial and nuclear) Tsinghua
(China)
- Specific sites
- ANTIGENIC (finds antigenic sites in proteins) Pasteur
(France)
- CANSITE (Protein Substrate Site Search and Prediction: Tyrosine, Serine
Kinase, PDZ domain) SDSC
- ChloroP (identification of chloroplast transit peptides and their
cleavage sites) CBS (Denmark)
- Compep (predict peptides (complements) that may bind the target) BRUS
(Singapore)
- 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
- 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)
- 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)
- ProPred (predicts MHC Class-II binding regions) Chandigarh
(India)
- SIGCLEAVE (signal cleavage sites) Pasteur
(France), see also UMMS
(USA)
- TargetP (predicts the subcellular location of eukaryotic protein
sequences) CBS
(Denmark)
- ZZIP (Leucine Zipper Prediction) TBI
(Germany), see also Montpellier
(French)
- Transmembrane regions
- DAS Stockholm
(Sweden)
- HMMTOP Budapest
(Hungarian)
- kPROT Weizman
(Israel)
- PHAT (Sequence Comparison for Transmembrane Sequences) FHCRC
(USA)
- PredTmr (predicts transmembrane segment in proteins) Athens (Greece)
- PSIPred server (MEMSAT) Warwick, see also
Brunel (UK)
- TMAP MBB
(Sweden)
- TMAP Pasteur
(France)
- TMHMM (CBS) V1.0, see also
V2.0
(Denmark)
- TMPred ISREC
(prediction of membrane-spanning regions and their orientation by
statistical analysis of TMbase)
- TopPred 2 (orientation and location of transmembrane helixes) Stockholm (Sweden),
see also Pasteur
- TSEG (Prediction Tool for Transmembrane SEGment in Proteins) Kyoto (Japan)
- SOSUI TUAT
(Japan)
- Structure 3D
- 3D-PSSM (Protein Fold Recognition (former Foldfit)) BMM (UK)
- Bioinbgu (fold-recognition based on Sequence-Derived Properties) Ben Gourion
(Israel)
- ClusProt (spatial clusters in protein structures on the basis of atomic
contacts between residues) Home
page, query
PDB sequences only (Heidelberg)
- Confmat (side chain packing optimization) Pasteur
(France)
- 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) Heidelberg,
see also Pasteur
- Domain Assignment BMM
(UK)
- DomainParser ORNL (USA)
- Environ (accessible as well and buried surface area) Pasteur
(France)
- Fold prediction 3D (based on homologous sequence search) EMBL (Germany)
- 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)
- LOOPP (aligns sequence to sequence, sequence to structure, and structure
to structure) Cornell (USA)
- MaxSprout (generating protein backbone and side chain co-ordinates from
a C(alpha) trace) EBI (UK)
- 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, see
also BCM-LPT
- SCMF (Homology Modelling Program) Pasteur
(France)
- STRIDE EMBL
(search secondary structures in proteins from atomic coordinates) : query,
see also Pasteur
- 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)
- 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 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 Zurich
- AMAS (read an alignment to enhance conserved aminoacids) Barton
group (EBI)
- AVID (align two sequences) Berkeley (USA)
- 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
- ComAlign: Combining many multiple alignments in one improved alignment
Pasteur
(France)
- Consensus (calculates the consensus for the CLUSTAL or MSF multiple
alignment) EMBL
(Germany)
- CRASP (Correlation Analysis of Sequences of Proteins) MBS
(Russian)
- 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)
- 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
- GLASS (aligning pairs of homologous sequences) MIT (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)
- 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), see also Genoscope
- LFasta (Local Alignment Tool for Nucleic Sequences) ACNUC (France)
- Map123d (Global multiple Alignment) Bio-lirmm
(France)
- 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)
- MBS Aligner MBS (USA)
- MSA (Ctree, MSA, Clustal) IBC (USA)
- 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
- NEEDLE (Needleman-Wunsch global alignment) Pasteur
(France)
- Pairwise Global Alignment NYU
(USA)
- Pairwise Sequence Alignment (SIM, GAP, NAP) Michigan (USA)
- Pairwise Sequence Alignment (SIM, ALIGN, BLAST, LAP2, PCWISE, PCWISE) BCM
- PIMA (Align a Query Sequence against a PIMA Multiple Alignment using
PIMA) BCM
- PIMA (Pattern-Induced Multi-sequence Alignment program) Pasteur
(French)
- PipMaker (alignments of similar regions in two DNA sequences) Pennsylvania (USA)
- PLALIGN (alignment of 2 sequences) Virginia
- PRSS (evaluate the significance of a protein or DNA sequence similarity
score) EMBNet
- SAM UCSC
( linear hidden Markov model), documentation,
see also Pasteur
- SIM : Alignment Tool for 2 sequences protein
sequences, nucleic sequences
(Expasy)
- SSEARCH Pairwise Sequence Alignment PIR
(USA)
- SSAS (Secondary Structure Alignment Server) Rutgers (USA)
- 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
also GPRC
- ToPLign (standard pairwise and multiple alignment methods) GMD (Germany)
- WATER (Smith-Waterman local alignment) Pasteur
(France)
- WORDMATCH (finds all exact matches of a given size between 2 DNA
sequences) Pasteur
(France)
- 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)
- FastDNAml Pasteur,
see also advanced
form, see also InfoBioGen
- HIV/SIV phylogenetic analysis ANRS
(France)
- LVB (Reconstructing Evolution With Parsimony And Simulated Annealing) Pasteur
(France)
- Molphy (ProtML, NucML, ProtST, NJDist) Pasteur
(France)
- Phylodendron (phylogenetic tree printer) IUBIO
(USA)
- Phyloquart (parciquart, distquart, qstar, addquart) Pasteur
(France)
- Phylogenetic tree prediction (from an alignment) Moscow
- PHYLIP
- Principal Coordinates Analysis Lyon (France)
- Puzzle (Tree reconstruction for sequences by quartet puzzling and
maximum likelihood) Pasteur,
advanced form
(France)
- Pyramids (pyramidal analysis tool for sequence clustering) Pasteur
(French)
- QR2 Pasteur
(French)
- RecPars (Parsimony analysis of DNA sequences) Aarhus
(Denmark)
- RETREE (unroot a tree) Pasteur
(French)
- ROSE (Random-model Of Sequence Evolution) Bielefeld
(Germany)
- SeqGen (Simulation of DNA sequence evolution) Pasteur
(France)
- 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)
- Weighbor (Weighted neighbor joining) Pasteur
(France)
Others
- Genetic
- IMpRH Web Server INRA
- LIAN (tests the null hypothesis of linkage equilibrium for multilocus
data) Max-Planck
(Germany)
- Linkage Analysis Server Cagliari
- MAP-O-MAT (marker-based linkage mapping server) Rockfeller
(USA)
- QGE gSCAN Hutchinson
(USA)
- ABS (QL prediction, MUSEQAL, Clustal, GOR4, FoReSST) NIH (USA)
- 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) EBI (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)
- BiBiServ Sequence Analysis Department Bielefeld
(DCA, GeneFisher, RIFLE, ROSE, Splits tree) (Germany)
- Biocomputing Resources by BRUS technology group BRUS (Clustalw, GCG, Patscan, Phylip,
Primer, Promoteur Scan, Signal Scan)
- 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 Toolkit (Blast, Fasta, Clustalw, PredictProtein, SEWER
interface) CMBI
(Netherlands)
- Bioinformatics Tools (P-SEA, TITO, MODELLER, SMD, CHECKMODEL) InfoBioSud
(France)
- Biological programs accessible through the Web server of Pasteur (France)
- Biomolecular Modelling Laboratory (Sawted, Foldfit, 3D-PSS, Multidock,
Ftdock, Loop, Dsc) BMM
(UK)
- BITMed Simulators (Game of life, Wave rule, Genetic algorithm, Dendritic
Growth ...) UCSD
(USA)
- BLA (BioLirmm Assistant) a workbench for molecular biologists LIRMM (France)
- BLASTULA (the server of Blast servers) GIFTS
(France)
- The Brutlag Bioinformatics group (emotif, identify, scan, decypher, alion)
Stanford (USA)
- CBC protein analysis (PANAL) CBC (Prosite,
Blocks, Prints, Pfam) (USA)
- CombSearch (unified interface to query several protein identification
tools accessible on the web) CUI
(Switzerland)
- Computational Biochemistry Research Tools ETH (Darwin, AllAll, AllAllDB,
MassSearch, MultAlign, NuclPepSearch, PepPepSearch, TreeGen)
- Computational Biology IBM Research
(USA)
- Computational Biosciences Tools (GenQuest, Grail) Oak Ridge (USA)
- Computational Services developed and offered by EMBL (ASC,
ClusProt, OBSTRUCT, PredictProtein, PROPSEARCH, SSCP, SSPRED, STRIDE, TMAP),
see also "Argos
service", see also Comparative Sequence Analysis Bork's group
(Heidelberg)
- Computer Programs (RGSites scan, Predicting activities of functional sites
in DNA/RNA, CRASP, CRAFT) MBS (Russian)
- 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)
- 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)
- GeneBee services Moscou
- Genestream (Blast, Fasta, Align, LFasta, LAlign, SSearch, Map ...), see
also IGHM (France)
- Genomic analysis Web Tools Sanger (UK)
- HIV/SIV phylogenetic analysis (blast, alignment, tree, recombinant) ANRS
(France)
- HMM Applications (Compare, Query, Tune Up : hidden Markov model) UCSC
(USA)
- IBM Bioinformatics Groups (Protein annotation, MSA, Pattern discovery,
Gene identification...) IBM
- Integrated Analysis Services (with registration) HGMP (BLAST, NIX,
GLUE, PIE, RHyME, MAGI)
- ISREC Software Homepage (Lausanne) ISREC
(BOXSHADE 3.0, Coils, EPFL-BLAST, PatternFind, ProfileScan, PrositeScan, SAPS,
TMPred)
- Jade development environment and demos Montpellier
(France)
- Java-based Molecular Biology Work Bench EMBL
(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 (France)
- LPT (GeneFinder, Prosite, 123D, SARF...) BCM-LPT (USA)
- 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...) Heidelberg
(Germany) (requires File Upload mechanism : Netscape)
- NCBI (PubMed, Entrez, BLAST, BankIt, OMIM, Taxonomy, Structure) NCBI (USA)
- NCSA BIOLOGY WORKBENCH NCSA (Database Search, Blast,
MSA), see alsothe new
version
- NetMul PBIL (online
multivariate analysis system)
- NIMR Tools (Quest, Humanisation, Mview, Praline, Repro, Tune1D) NIMR (UK)
- NPS@ (Network Protein Sequence @nalysis) PBIL
(France)
- On-line Resources From UMBER (Align, Bioactivity, Cinema, Easy,
FingerPRINTScan, PRINTS) Manchester (UK)
- 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)
- Prediction servers (CPHmodels, HMMgene, NetGene, NetOglyc, NetPicoRNA,
NetPlantGene, NetStart, SignalP) CBS (Denmark)
- 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 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)
- 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) Warwick (UK)
- RDP-II Online Analyses (Probe, Align, Distance, Chimera, T-RFLP,
SubTrees..) CME
(USA)
- Sequence Analysis & Tools at Stanford (USA)
- (Blast, Fasta, Primer, PatMatch, Restriction, SAGE, Similarity View..)
S.
cerevisiae
- (Blast, Fasta, Primer, PatMatch, Restriction..) Arabidopsis
(TAIR)
- 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 MDC (Blast, Adops, Idsecs, SOM-X) MDC (Germany)
- Similarity Search Engines ProWeb
(USA)
- Structural Bioinformatic (Meta-Server, P-Sea, TITO, Modeller, SMD, W-Loop,
3D-Evaluatio, LEA) Montpellier
(French)
- Structure Prediction sever (Gons, Alignments, Profiles, 123-D prediction
...) UCLA-DOE (results by
e-mail)
- STS Pipeline v1.2 (Whitehead Institute) MIT (Vector-stripping,
Microsatellite-finding, BLAST, Restriction Analysis, Primer-picking)
- 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)
- TOPS (Protein Topology : search, compare, cartoon..) EBI (UK)
- TRADAT (TRAnscription Databases and Analysis Tools) MI (Italy)
- TRANSFAC (MatInspector, FastM, PatSearch, SaGa, Clustalw, Boxshade,
FunSiteP) GSF (Germany)
- USC Computational Biology USC (Alignment,
Chimera, Gene Recognition)
- Virtual Genome Center (Alces) VGC (Coding region,
Dotplots, Dst, Oligo Tm, Primer, Zinfo)
- WebGene Server ITBA (Italy) (Gene
prediction, Splice, Poly A, Tata Box, MSA)
- wEMBOSS IBBM
(Argentina), see also PBI (Canada), see
also EBI
(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)
- Index
- Analysis tools Pasteur
(France)
- Biotechnology Software NBIF (USA)
- DNASYSTEM (Sequence Analysis Site) San
Diego (USA)
- The DEAMBULUM (Optimized Maze in Molecular Biology) InfoBioGen
(France)
- Similarity Search Engines Proweb
(USA)
- Software Seek genamics (USA)
Utilitaries
- BLAST output to FASTA format NIH (USA)
- BOXSHADE Pretty Printing and Shading of Multiple-Alignment files EMBNet, see
alos Pasteur
(France)
- Drawseq - biosequence drawing tool Indiana
(USA)
- Fmtseq (sequence conversion) Pasteur
(France)
- GB2xml (Genbank to XML conversion tool) Pasteur
- MuSeqBox (Multi-query Sequence Blast output examination) ISU
(USA)
- Lowercase low-complexity regions (PSEG) Virginia
(USA)
- The Alignment Colour Viewer EBI (by deafult,
colour an alignment of two protein sequences according to the aminoacids
hydrophobicity: settings change available)
- The Protein Colourer EBI (by
default, colour aminoacids according to their hydrophobicity : settings change
available)
- PrettyPlot MulSeqs UMMS (USA)
- Rapid Sequence Visualization in PostScript RSVP
(Pennsylvania)
- Reformat sequences Wisconsin
(USA)
- 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
ABIM
Biology Home Page