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Bioinformatics Links

links to informatics resources on the net

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The main list is maintained by ICP and has been mirrored with their permission. Compiled by Mark Van Ranst(KUL). Updated and adapted for use on the internet by Fred Opperdoes(UCL). Please report broken links to FredOpperdoes

BioInformatics Links
DNA/PROTEIN DATABASES GENERAL DATABASE INFO
Database Statistics (courtesy of DDBJ) Human Genome Sequencing GENBANK (NCBI) GENBANK SITEMAP EMBL (EBI) PDB Protein 3D database Nucleotide sequences at EBI Nucleotide sequences at GenBank MAGPIE - Multipurpose Automated Genome Project Investigation Environment DDBJ (DNA Data Bank of Japan) MBGD Microbial Genome Database HOX Pro DataBase (in Russia) HOX Pro DataBase (Mirror in the US) Expasy Home of SwissProt Protein database SWISS-PROT (ExPasy) The Sanger Centre		Genome Monitoring Table (daily update EBI) MAGPIE NIH News Release 06/26/2000 Enzyme Nomenclature TIGR Microbial Database Pfam Protein domain database at Sanger Centre The TIGR Trypanosoma brucei Database Trypanosome GeneDB at Sanger BMERC Completed Genomes collected resources DNA Sequence Collaborator's Page Genome Sequence Database GSDB (NCGR) PEDANT complete genome analysis C. elegans Database The Protein Research Foundation Population studies with PopSet with aligned DNA seqiences Extinct organisms in GenBank DBGET Database Document: GenBank
SEQUENCE SUBMISSION
GENBANK BankIt GENBANK Sequin EMBL Webin DDBJ Sakura		Vector screening VecScreen (NCBI) Vector Scanning (EBI) Vector Screening System (DDBJ)
SEQUENCE RETRIEVAL
DNA ENTREZ-Nucleotide query (NCBI) SRS at EMBL-EBI, Hinxton (UK) DNA Search (GenomeNet, Japan) GENBANK at NCBI Direct retrieval from EMBL via accession code	PROTEIN
	ENTREZ-Protein query (NCBI) SRS at EMBL-EBI, Hinxton (UK) Protein Search (GenomeNet, Japan) SWISS-PROT and TrEMBL (Switzerland) RCSB Protein Data Bank (US) RCSB PDB Mirror Sites PIR-Web - The Protein Identification Resource (NONACTIVE) GENBANK using ENTREZ Protein Search (GenomeNet, Japan) Direct retrieval from EMBL via accession code
ALERT SERVERS EMBL Sequence Alerting System SWISSPROT alert server BEN sequence awareness service (registered users only) BEN sequence similarity awareness service (registered users only)

GENOMICS GENERAL GENOMICS
Entrez-Genome (NCBI) Genome Monitoring Table (daily update EBI) NCGR National Center for Genome Resources Genome Channel (Oak Ridge, US) *			Organism-specific Databases GOLD: Genomes OnLine Database Homepage PEDANT front page NIH News Release 06/26/2000 The Human Genome, by All of the Top Cartoonists
HUMAN GENOME PROJECT
NIH/NCBI HUMAN GENOME RESOURCES The Human Genome Entrez Genome view: MAPVIEWER LocusLink Introduction Human Genome Sequencing National Human Genome Research Institute (NHGRI) dbSNP Home Page NCBI Contig Build and Annotation Process ENSEMBL (EBI/Sanger Institute) Ensembl Genome Server (not active) HUGO (Human Genome Organisation) HUGO homepage HUGO human chromosomes page HUGO Gene Nomenclature Committee (HGNC) OMIM (Online Mendelian Inheritance in Man) OMIM - Online Mendelian Inheritance in Man DDBJ/CIB HUMAN GENOMICS STUDIO DDBJ/CIB Human Genomics Studio			GENECARDS GeneCards (Weizmann Institute, Israel) GeneCards mirror (Finland) GeneCards mirror (Germany) GeneCards mirror (Canada) GeneCards mirror (Japan) HGSC Human Genome Sequencing Center (Baylor College of Medicine) Welcome to Baylor HGSC ONL Oak Ridge National Laboratory Human Genome Landmarks Poster Human Genome Project Information ETHICAL, LEGAL, SOCIAL ASPECTS Clinical and patient aspects (HUGO) Ethical, Legal and Social Implications (ELSI; NHGRI at NIH)
OTHER GENOME PROJECTS
EUKARYOTIC GENOME PROJECTS Mouse Genome Resources Page Rat Genome Resources Page Zebrafish Genome Resources Page Drosophila melanogaster @ NCBI Malaria Genetics & Genomics C. elegans project Arabidopsis thaliana MICROBIAL GENOME PROJECTS PEDANT complete genomes Entrez: microbial genomes taxonomy tree TIGR Microbial Database DDBJ Genome Information Broker VIRAL GENOME PROJECTS Complete viral genomes (NCBI) Retroviruses			PARASITE GENOME PROJECTS Trypanosoma brucei Genome Project Leishmania Genome Network Trypanosoma brucei home page (at Sanger) T rypanosoma brucei Genome Network home page Trypanosoma brucei GSS sequences for downloading The TIGR Trypanosoma brucei Database Trypanosome GeneDB at Sanger Trypanosoma cruzi Blast search at TIGR Leishmania major home page (at Sanger) Leishmania Genome Network home page Leishmania major chromosome 15 Leishmania major chromosome 26 Leishmania major chromosme 28 Leishmania Genome Network, Seattle, USA Parasite-genome database at EBI Parasite genome Blast server at EBI Parasite genomes databasesWHO Leishmania Genome Network Web site Malaria (Plasmodium falciparum genome map) Plasmo DB (Plasmodium Genome database)
COMPARATIVE GENOMICS
PEDANT CrossGenome categories COG: Clusters of Orthologous Groups of proteins( NCBI) TaxPlot (NCBI) HOBACGEN Homologous Bacterial Genes Database			WIT Home Page KEGG Kyoto Encyclopedia of Genes and Genomes ERGO (Integrated Genomics, Inc.) LION bioscience \| Products and Services \| genomeSCOUTô
COMPLETE GENOMES AND GENOME PROJECTS
GOLD Genome On line Database Proteome analysis at EBI All Available Complete Genomes GeneQuiz (Genome annotations) LocusLink (Human, Mouse and Rat Loci) Entrez Genomes Views (Human Chromosomes) Mitochondrial Genomes Database GOBASE - The Organelle Genome Database Saccharomyces Genome Database Mycoplasma genitalium database (not available) Haemophilus influenzae database (not available) Methanococcus jannaschii database (not available) E. coli genome center Heliobacter pylori database (not available) E. coli database collection (not available) Sanger Center C. elegans homepage (not available) Bacillus subtilis database Genome Sequencing Center, St. Louis			Methanobacterium thermoautotrophicum abstract The Genome Database Sanger Center S. pombe homepage (not available) Human Genome Project Infor Mouse Genome Database mation (not available) Arabidopsis thalianaProject Arabidopsis genome completed (Nature paper, 2000) Flybase(not available) Drosophila database TIGR Arabidopsis thaliana Database TIGR Archaeoglobus fulgidus Database(not available) TIGR Borrelia burgdorferi Database(not available) Pyrococcus furiosus news article Pyrobaculum aerophilum abstract(not available) Sulfolobus solfataricus P2 complete genome Borrelia burgdorferi news article Yersinia Pestis complete genome HOBACGEN (the Homologous Bacterial Genes Database)
TAXONOMY
NCBI Taxonomy Homepage Taxonomy Browser at NCBI The Tree of Life Home Page Introduction to Phylogeny			RIBOSOMAL RNA Ribosomal Database Project II (USA) The rRNA WWW Server (UIA Antwerp)
DNA SEQUENCE ANALYSIS GENE PREDICTION EMBOSS at EBI Gene Finder at Sanger centre PredictGenes (Darwin) (Switzerland) SBDS sequence analysis Bipartite Nuclear Localisation Sequence Locator IUPAC-IUB Abbreviations and symbols for nucleic acids, polynucleotides and their constituents. GENSCAN at MIT (US) * WebGeneMark GrailEXP at Oak Ridge (US) Genie at Berkeley (US) Gene Prediction Services TRANSLATION EMBOSS at EBI ExPASy - Translate tool DNA Sequence Translation (ALCES) The Protein Machine (EBI) Nucleic Acid to Amino Acid Translation (London) Nucleic Acid to Amino Acid Translation (London - mirror) SeWeR is a DHTML interface for web based sequence analysis IUBMB Prokaryotic and eukaryotic translation factors. ORF ANALYSIS EMBOSS at EBI ORF Finder (NCBI) ORF analysis (WebGene) FGENESH-2 Improving gene finding accuracy FGENESH HMM - Gene finding for mouse genes TRANSCRIPTION FACTOR BINDING SITES TFSEARCH: Searching Transcription Factor Binding Sites MatInspector (Germany) Alibaba2 (Germany) REPEATS EMBOSS at EBI Dot Plot Analysis THEORETICAL EXPLANATION Dot Plots (Colorado State University) (limit: 20.391bp x 20.391 bp) Dot Plot (to itself) (ALCES) (postscript/GIF output) Blast 2 Sequences (NCBI) CODON USAGE Codon Usage Database Codon usage (ALCES) GCUA (Thomas Schoedl's Graphical Codon Usage Analyser) CONTIG ASSEMBLY CAP sequence assembly at Infobiogen CAP Sequence Assembly at BCM Search Launcher PATTERN SCAN PatScan RESTRICTION ENZYME RE ANALYSIS Webcutter 2.0 (USA) Webcutter 2.0 (USA) Webcutter 2.0 (Sweden) Restriction Enzyme Analysis (SUNY) (US) Restriction Maps (Colorado) (US) REMAP MBS - SeqCUTTER - On-line enzyme restriction analysis tool MULTI-CUT Restriction Endonuclease Buffer Data Base RE LISTS REBASE at NEB RE SUPPLIERS Restriction Endonuclease Suppliers (Multi-Cut site) OLIGO/PRIMER ANALYSIS WWW GeneFisher (Germany) * PCR Aplification Assistant IDT OligoAnalyzer 2.0 (US) * Oligonucleotide Calculator (USA) - simple GENSET OLIGOS - Oligo Calculation Tm Determination (ALCES) - simple pDRAW32 - freeware DNA cloning, sequence analysis and plasmid/DNA plotting software Oligonucleotide Calculator (USA) - simple WWW GeneFisher Primer3 at MIT (US) Primer3 (older version) Primer Selection (Text) (ALCES) NetPrimer (US) NCBI Blast short sequence Visual Cloning 2000 (Redasoft) PCR Box Titration Calculator v 0.93 Alkami Biosystems: Primer Design Online Web Primer: DNA and Purpose Entry CODEHOP netprlaunch Tavi's PCR protocols SIMPLE NUCLEOTIDE MANIPULATIONS Reverse/Inverse/Inverse complement (Colorado State University) BCM: Sequence Utilities (inverse, complement) MBS - SeqCLEANER - Clean up your sequences from databases marks The Sanger Centre : Java View ABI traces at Sanger PROTEIN SEQUENCE ANALYSIS EMBOSS at EBI Match-Box server HOX Pro DataBase (in Russia) HOX Pro DataBase (Mirror in the US) PirAlin protein alignment database Entrez-Protein SWISS-PROT and TrEMBL PIR-Web - The Protein Identification Resource Protein Search (GenomeNet, Japan) PirAlin protein alignment database Enzyme Nomenclature Pfam Protein domain database at Sanger Centre Darwin, a Computational Biochemistry Research Tool Readseq - biosequence conversion tool SeWeR is a DHTML interface for web based sequence analysis AMINO ACID/PROTEIN INFORMATION Genetic Code Viewer single letter amino acid codes amino acid structures BRENDA the enzyme database IUBMB enzyme nomenclature IUPAC-IUB: phosphorus-containing compounds of biochemical importance IUPAC-IUB : synthetic polypeptides - Polymerised amino acids. HYDROPHOBICITY PLOT Hydropathicity Plots at Colorado (US) REVERSE TRANSLATION Reverse Translate a Protein at Colorado (US) MOTIFS / PATTERNS SEARCHING NPS@ : PATTINPROT search PROSITE at EBI (Hinxton, UK)) PROSITE at ExPASy (Switzerland) PRATT at EBI (input alignment) * FPAT Regular Expression Searching Protein Databases MIPS ATLAS PatScan (also imperfect matches) ISREC PatternFind (WWW to EMAIL) Motif Explorer N-Glycosylation Site Prediction Server CBS prediction servers BNL motif searching SignalP signal peptide identification Sigfind signal peptide identification MOTIFS in SwissProt at IBCP (France)(WWW to EMAIL) PRINTS BLOCKS PRODOM SBASE MOTIF at GenomeNet (Japan) Protein Motifs (ALCES) PROTCOMP Identification of sub-cellular localization of eukaryoric proteins GENEQUIZ GQserve - Public GeneQuiz Server *** PREDICTPROTEIN The PredictProtein server PPstatus: What is the PP backlog ? DARWIN Darwin, a Computational Biochemistry Research Tool TreeGen: Tree generation from distance data AllAll: Related peptide sequences AllAllDB: Querying the all-against-all database of SwissProt NuclPepSearch: Searching SwissProt for a nucleotide sequence PepPepSearch: Searching SwissProt for a peptide sequence darwin: Run a Darwin program STATISTICAL ANALYIS Statistical Analysis of Protein Sequences at EBI (Hinxton, UK) SAPS at ISREC (Switzerland) DIGESTION PRODUCTS SEARCH MOWSE PROWL MassSearch: Searching SwissProt or EMBL by protein mass after digestion PROTEIN SORTING / LOCALIZATION PSORT (Japan) PROTCOMP Identification of sub-cellular localization of eukaryoric proteins SignalP signal peptide identification ISO-ELECTRIC POINT / MOLECULAR WEIGHT protein -> pI, MW and Composition protein -> pI and MW (EXPASY) AMINO ACID COMPOSITION Protein -> AA composition (SBDS) Protein -> AA composition + analysis (SAPS at ISREC) AA composition -> protein search (EXPASY) AA composition -> protein search (EMBL) AA composition -> Sec. Str. (EMBL) (WWW to EMAIL) MBS - ProtCALC - protein parameters (pI, MW, aa composition, Extinction data) ProtoMap - Main CGG Protein sequence analysis METABOLIC PATHWAYS			SEQUENCE ALIGNMENT SEQUENCE-FORMAT CONVERSION Readseq - biosequence conversion tool Readseq - at Iubio Indiana USA PAIRWISE SEQUENCE ALIGNMENT BCM: Pairwise Sequence Alignment Dot/matrix plots Dotmatrix program PPCMatrix LALIGN (france) Blast 2 Sequences (NCBI) SBDS: Pairwise Sequence Alignment (works only well for proteins) MBS - ALIGNER : CLUSTALW interface for multiple sequence alignement (did not work on netscape navigator) MULTIPLE SEQUENCE ALIGNMENT BCM: Multiple Sequence Alignments IBC: Multiple sequence alignment (MSA) SAM: Sequence Alignment and Modeling System CLUSTALW at GenomeNet (Japan) ClustalW at EBI (UK) CLUSTALW at DDBJ (Japan) CLUSTALW at IBCP (WWW to EMAIL) GeneBee ClustalW 1.75 CMBI CLUSTAL W MULTALIN at IBCP (WWW to EMAIL) MULTALIN + CLUSTAL at IBCP (WWW to EMAIL) ALIGNMENT VISUALISATION/EDITING/FORMATTING BoxShade Server (Switzerland) *** ForCon homepage CINEMA (Colour INteractive Editor for Multiple Alignments) SEQUENCE HOMOLOGY SEARCHES BLAST BLAST at NCBI (USA) - basic BLAST at NCBI (USA) - advanced BLAST against (un)finished Genomes at NCBI (USA) MEGABLAST at NCBI (large set of DNA query sequences) MEGABLAST at Harvard (large set of DNA query sequences) Search for short nearly exact matches of DNA sequences Search for short nearly exact matches of protein sequences PSI BLAST at NCBI (USA) - Position Specific Iterated BLAST BLAST 2 sequences BLAST at EBI (Hinxton, UK) BLASTall at EBI (Hinxton, UK) BLAST at GenomeNet (Japan) BLAST at BCM: DNA searches BLAST at BCM: Protein searches BLAST at PIR-International Protein Sequence Database BLAST search in PRODOM OWL BLAST Server GeneBee Basic BLAST 2.0 Genebee Advanced BLAST 2.0 FASTA FASTA at EBI (Hinxton, UK) FASTA at NPS (France) FASTA Email server at EBI Fasta 3.3 SW (Smith-Waterman) Smith-Waterman (EBI) BASED ON AA COMPOSITION AA composition: protein search (ExPASY) AA composition: PropSearch (EMBL) DARWIN AllAll: Related peptide sequences AllAllDB: Querying the all-against-all database of SwissProt NuclPepSearch: Searching SwissProt for a nucleotide sequence PepPepSearch: Searching SwissProt for a peptide sequence PROPSEARCH (EMBL) (WWW to EMAIL) EMBL Dali: email server for 3-D protein structure database searches SECONDARY/TERTIARY STRUCTURE PREDICTION RNA RNA folding (Zuker) RNA folding (Zuker, older version, allows variable temp) RNA folding (Zuker; mirror at Wayne State University) RNA folding (Zuker; mirror in Australia) returns results by email only. PROTEIN AGADIR An algorithm to predict the helical content of peptides SSCP Secondary structural content prediction from amino acid composition Southampton - SBDS - GOR CPHmodels - Homology modelling PREDATOR request form Southampton - SBDS - GOR IBCP secondary structure (France) Protein Explorer FrontDoor (Univ Mass) Protein Explorer FrontDoor (San Diego, faster) PredictProtein 3D-PSSM Protein Fold Recognition (Threading) Server (UK) Description of SSThread WWW service GENO3D : AUTOMATIC MODELING OF PROTEINS THREE-DIMENSIONAL STRUCTURE BCM: Secondary Structure Prediction PREDATOR request form EMBL Dali: email server for 3-D protein structure database searches BCM PSSP CE Home Page - Combinatorial Extension SSCP: protein -> AA composition -> SS (EMBL) (WWW to EMAIL)

Bioinformatics Links

links to informatics resources on the net

GENERAL DATABASE INFO

SEQUENCE SUBMISSION

SEQUENCE RETRIEVAL

ALERT SERVERS

GENOMICS

GENERAL GENOMICS

NIH/NCBI HUMAN GENOME RESOURCES

ENSEMBL (EBI/Sanger Institute)

HUGO (Human Genome Organisation)

OMIM (Online Mendelian Inheritance in Man)

DDBJ/CIB HUMAN GENOMICS STUDIO

GENECARDS

HGSC Human Genome Sequencing Center (Baylor College of Medicine)

ONL Oak Ridge National Laboratory

ETHICAL, LEGAL, SOCIAL ASPECTS

EUKARYOTIC GENOME PROJECTS

MICROBIAL GENOME PROJECTS

VIRAL GENOME PROJECTS

PARASITE GENOME PROJECTS

RIBOSOMAL RNA

TRANSLATION

ORF ANALYSIS

TRANSCRIPTION FACTOR BINDING SITES

REPEATS

CODON USAGE

CONTIG ASSEMBLY

PATTERN SCAN

RESTRICTION ENZYME

RE ANALYSIS

RE LISTS

RE SUPPLIERS

OLIGO/PRIMER ANALYSIS

PROTEIN SEQUENCE ANALYSIS

AMINO ACID/PROTEIN INFORMATION

HYDROPHOBICITY PLOT

REVERSE TRANSLATION

MOTIFS / PATTERNS SEARCHING

GENEQUIZ

PREDICTPROTEIN

DARWIN

STATISTICAL ANALYIS

DIGESTION PRODUCTS SEARCH

PROTEIN SORTING / LOCALIZATION

ISO-ELECTRIC POINT / MOLECULAR WEIGHT

AMINO ACID COMPOSITION

METABOLIC PATHWAYS

SEQUENCE ALIGNMENT

PAIRWISE SEQUENCE ALIGNMENT

MULTIPLE SEQUENCE ALIGNMENT

ALIGNMENT VISUALISATION/EDITING/FORMATTING

SEQUENCE HOMOLOGY SEARCHES

BLAST

FASTA

SW (Smith-Waterman)

BASED ON AA COMPOSITION

DARWIN

SECONDARY/TERTIARY STRUCTURE PREDICTION

RNA

PROTEIN