Index of Resources:

Sequence Analysis: Guides, Tutorials, & Primers

Major genomic servers

Computational genefinding

Phylogenetic Analysis

Database Retrival Systems

Sequence Comparison, Homology Searches

Sequence Homology Searches

General Multi-Motif Search

Peptide Binding Prediction

Post-Translational Modification

Signal Peptide Motifs

Transmembrane Spanning Motifs

Transcriptional Factors/Elements

Protein Homology-Domains and Motifs/Patterns Databases

Sequence Alignment Servers & Databases

Multifunction Protein Sequence Analysis Tools

Sequence Presentation Tools

• BioActivity- excelent web paractical in Bioinformatics at UCL (UK).
• Bioinformatics course (C40) - organised by Terry Atwood UCL
• GNA-VSNS - Summer 1996 GNA-VSNS Biocomputing Course at Bielefeld (Germany)
• Training programs in bioinformatics and computational biology worldwide - kept in ISCB (International Society for Computational Biology)
• Bioinformatics tutorials list - kept at CCP11 (UK)
• Homology modelling course - by G. Vriend's gang (EMBL)
• Guide to Sequence Searching
• Protein Sequence Alignment & Database Scanning - excelent text by Goeffrey Barton.
• Sequence alignment primer - by Boris Steipe (EMBL)
• Database Search - by Keith Robinson (EMBL)
• Genome Analysis: A laboratory Manual (CSHL Press)
• Phylogenetic analysis - at ABA Bioinformatics

• The Sanger Centre - (Cambridge,UK)
• PEDANT - (Munchen, Germany)
• Human Genome Project - Genetics
• NCBI - USA
• UK Human Genome Mapping Project; Resource Centre
• The Human Transcript Map
• Computational gene-finding - link to Anders Krogh's page

• Arabidopsis thaliana database at Stanford

• Computational Gene Recognition - (Rockefeller, New York)
• Functional Analysis of Nucleotide Sequence Reference Data Bank -
•  Computational gene-finding - link to Anders Krogh's page

• AAT - gene identification or prediction server at Michigan Tech.
• MZEF - (Michael Zhang's Exon Finder) an internal coding exon predictiton program by quadratic discriminant analysis
• FGENEH - V.V. Solovyev's program based on pattern recognition at Sanger Centre
• GenLang Linguistic Sequence Analyzer - pattern-matching search of DNA sequences using principles of computational linguistics - Dong and Searls at U. Pennsylvania.
• GeneID-3 - Gene Identification and Gene Structure Prediction in Genomic DNA Sequences at Barcelona
• GeneParser - a program for the identification of protein coding regions in genomic DNA sequences.
• GLIMMER - (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA at JHU
• MORGAN - an integrated system for finding genes in vertebrate DNA sequences at JHU
• GRAIL - (Gene Recognition and Assambly Internet Link) at ORNL
• NetGene2 - neural network predictions of splice sites in human, C. elegans and A. thaliana DNA at CBS (DK).

• Genie - A Gene Finder Based on Generalized Hidden Markov Models
• HMMgene - Anders Krogh's program
• GENSCAN - at Stanford
• GeneMark and GeneMark.hmm at Georgia Inst. Tech.
• Veil - (the Viterbi Exon-Intron Locator) uses a custom-designed hidden Markov model (HMM) to find genes in eukaryotic DNA at JHU.

Several programs available on the server in the Institute Pasteur

Few downladable programs:

• PAUP - Phylogenetic Analysis Using Parsimony
• PHYLIP - free package for inferring phylogenies, and very good references therein.
• Hennig86 - Parsimony analysis program available for MS-DOS
• GAMBIT -
• MacClade - a computer program for phylogenetic analysis.

• SRS - at EBI (UK)
• Entrez - at NCBI (USA)
• DBGET - Japan

• KEGG -
• LIGAND -
• WIT -
• EcoCyc -
• UM-BBD -

• A protein sequence search protocol - a systematic search strategy at UCL (UK)
• WWW READSEQ sequence converter

• BLAST - Basic Local Alignment Search Tool (& Information) at:
• BLAST2 - at EBI (UK)
• BLAST2 - NCBI (US) includes PSI-BLAST
• BEAUTY - returns BLAST hits + annotated domains (at BCM US)
• FASTA - Pearson and Lipman (Algorithm) Sequence Comparison Service (& Information) at;
• FASTA3 - EBI (UK)
• Smith-Waterman (Algorithm) Sequence Comparison Service at;
• Bic_sw (& Info) - EBI (UK)
• Scanps - at EBI
• BIOCCELERATOR - at EMBL

• Pattern and domain database search at UCL

• HMM Search - Motif Search of a Protein Sequence using the Pfam-A Database of Protein Domains at:
• HMM Search - WUSTL (US)
• HMM Search - Sanger Centre (UK)
• MOTIF - Patterns Search Service at;
• MOTIF - GenomeNet (Japan)
• MOTIF - Iowa State U (US)
• Pratt2.1 - Pattern Discovery Tool (& Info) at;
• Pratt - EBI (UK)
• PRODOM (Protein Domains Database) Analyses;
• PRODOM - Blast search through the protein families database constructed with the PSI-BLAST at Toulouse (France)
• Profile Server - Profile Motifs Search at SDSC (US)
• PROSITE - Protein Motifs Searches of ProSite Database at;
• PROSITE Search - EBI (UK)
• PrositeScan - ISREC (Switzerland)
• PrositeScan - EMBNET (Switzerland)
• ScanProsite - ExPasy (Switzerland)
• PROTFAM - Protein Sequence Homology (Super)Families Browser and Keyword Search Service at MIPS (Germany)
• PRINTS/PROSITE Scanner - Search PRINTS and PROSITE Databases with Query Sequence at UCL (UK)
• ProfileScan - Compare a sequence against PROSITE Motifs Database at ISREC (Switzerland)
• Protein Sequence Analysis - PROSITE at ICBP (France)
• Protein Sequence Motifs Search (Info) at the U Minnesota (US);
• PSMS-DNA - Determines if a Protein Motif is encoded by a DNA Sequence
• PSMS-PRO - Determines if a Protein Motif is present in a Database of Protein Sequences
• REPRO - Recognition of Protein Sequence Repeats Search Service at EMBL-Heidelberg (Germany)
• SSBASE Protein Domains Library Searching at;
• SBASE Blast - at ICGEB (Italy)
• SBASE Search (Based upon DB Entry Field Identifiers) at ICGEB (Italy)
• ScanProsite-2 - Search SwissProt Database with Custom Query or PROSITE Motif at Expasy (Switzerland)
• Search Pattern - Search for Sequence Pattern at U Claude Bernard Lyon1 (France)
• SeqhuntII - Search of Kabat Database with a Query Pattern/Motif at NWU (US)
• SPAPD - Screening Pattern or Alignment against a Protein databank at BIPCB-MSU (Russia)
• SwissShop - ProSite Information Query service at ExPasy (Switzerland)

• HLA Peptide Motif Search - HLA Peptide Binding Predictions (& Info) at BIMAS (US)
• Web Complementary Peptide - Prediction of Peptides that will Bind to a Query Sequence (& Info) at Nat U Singapore (Singapore)

• NetOglyc - Search query sequence for potential O-glycosylation sites at CBSA/Technical U Denmark (Denmark)
• PhosphoBase - Protein Phosphorylation Site Sequence Database at CBSA/Technical U Denmark (Denmark)

• PSORT - Predict Peptide Sorting Signals at GenomeNet (Japan)
• SignalP - Predict Signal Peptide Cleavage Sites at CBSA/Technical U Denmark(Denmark)

• DAS - Transmembrane Prediction from a Query Sequence at Biochem D-Stockholm U (Sweden)
• PHDhtm - Predict Transmemebrane Helices (& Info) at EMBL-Heidelberg (Germany)
• PHDtopology - Predict Topology (N-Terminal Orientation) of Transmemebrane Helices at ( & Info) EMBL-Heidelberg (Germany)
• SOSUI - Prediction of Transmembrane Regions at Tokyo U Ag & Techn (Japan)
• TMAP - Analysis of Protein Transmembrane Regions rom multiple sequence alignment at Karolinska Institut.
• TMPRED - Protein Transmembrane Region Prediction at;
• TMPRED - ISREC (Switzerland)
• TMpred - BCM (US)
• TopPred2 - Topology Prediction of Membrane Proteins at Biochem D-Stockholm U (Sweden)
• HMMTOP - new HMM based topology predictor (Hungary)
• TMHMM - another HMM based predictor at CBS Danmark.

• TFSEARCH - Transcription Factor Search at RWCP (Japan)
• Patern Search TRANSFAC/TRRD - Search TRANSFAC & TRRD Databases with Query Motif at GBF (Germany)
• SignalScan-TRANSFAC/TFD - Search TRANSFAC and TFD Databases for Transcriptional Elements in Query Sequence at:
• SignalScan - BIMAS (US)
• Web Signal Scan - Nat Univ Singapore (Singapore)
• SignalScan-IMD - Search IMD Database for Transcriptional Elements in Query Sequence at BIMAS (US)

• ATLAS Sequence Scan - SearchDatabases for User-defined (30 AA Sequence Max Length) Motif at MIPS (Germany)
• HHS - Systemic Sequence Classification Database (SwissProt/PDB) at IBC-WUSTL (US)
• PRINTS - Protein Motif Fingerprint Database at UCL (UK)
• PRODOM - Protein Domain Database at INRA Toulouse
• PROSITE - Patterns/Motifs Database (& General Information) at ExPasy (Switzerland)
• PUU Protein Domains Database at EMBL-Heidelberg (Germany)
• SBASE - Database of Annotated Protein Domain Sequences (& Information) at ICGEB (Italy)
• SWISSDOM - SwissProt entries in the PRODOM map of detected domains at EBI (UK)
• PFAM - HMM made protein domain database at Sanger Centre.

• ALIGN - Global Alignment of Two Sequences at;
• ALIGN - IGH (France)
• ALIGN - MIPS (Germany)
• AllAll - Server multi-allignment function at ETH-Z (Switzerland)
• CLUSTALW - Multiple Sequence Alignments (& Documentation) at;
• CLUSTAL W - at EBI (UK).
• CLUSTALW (MSA) - IBC-WUSTL (US)
• LALIGN - N-Best Two Sequence Local Alignment at GeneStream-CRBM (France)
• LFASTA - Fasta Two Sequence Local Alignment at EERIE-Nimes (France)
• MAP - Multiple Global Alignment of Sequences Using Iterative Pairwise Method at BCM (US)
• Match-Box - Multiple Sequence Alignment at U Namur (Belgium)
• MaxHom - Multiple Sequence Alignment at EMBL-Heidelberg (Germany)
• MSA 2.1 - Multiple Sequence Alignment:
• MSA 2.1 - Multiple Sequence Alignment (& Documentation) at IBC-WUSTL (US)
• MSA2.1 - BCM (US)
• MULTALIGN - Multiple Sequence Alignment Service (& Documentation) at IBCP (France)
• MUSEQAL2 - Berger-Munson Multiple Sequence Alignment at DCRT-NIH (US)
• PSCAN - Sequence Alignment using User-Specified Data Set at Biochem D, U Stockholm (Sweden)
• PIMA - Pattern-Induced Loacal Alignment at BCM (US)
• PIMAII - Global/Local Protein Sequence Alignment at BMERC-Boston U (US)
• Pairwise Sequence Alignment - BCM (US)
• Sequance Alignment Server - Smith-Waterman Sequence Alignment at USC (US)
• SEQNET - at Daresbury Lab. funded by BBSRC

• SAM - Sequence Alignment and Modeling Software System
• HMMer - profile HMMs for biological systems by Sean Eddy.

• Biology Workbench v1.4 at NCSA (US)
• DARWIN - Data Analysis and Retrieval With Indexed Nucleotide & Peptide Sequences (&HELP) at ETH-Z (Switzerland)
• SAPS - Statistical Analysis of Protein Sequences at ISREC (Switzerland)

• BOXSHADE - Pretty Printing and Shading of Multiple-Alignment Files at ISREC (Switzerland)
• The Protein Colourer - Adds residue-specific color enhancement to protein sequences at EBI (UK)

Compilation done by Pawel Herzyk at York Structural Biology Laboratory.