Organism Databases
English version of ABIM : Banques : génomes
Genomes and sequences
- Complete Genomes
- COGENT (COmplete GENome Tracking : a flexible data environment for computational genomics) EBI (UK), see also CoGenT++
- Complete genomes NCBI (USA)
- Completed Genomes at the EBI EBI (UK)
- Completed microbial genomes TIGR
- Completely sequenced genomes Rockfeller (USA)
- EMGLib (completely sequenced bacterial genomes and the yeast genome) PBIL (France)
- Fully Sequenced Genomes Present In The Public DataBases GOLD (USA)
- Integr8 (integrated views of complete genomes and proteomes) EBI (UK)
- PEDANT (Protein Extraction, Description, and Analysis Tool) MIPS (more 200 genomes) (Germany)
- E. Coli : Wisconsin (USA), see also Entrez (NCBI)
- Rfam (annotating non-coding RNAs in complete genomes) Saint Louis (USA), see also Sanger (UK)
- SACSO (Systematic Analysis of Completely Sequenced Organisms) Pasteur (French)
- TIGR : Genomes (USA)
- Yeast Genome Project (Complete genome) MIPS (Germany), see also Genome Viewer, see also Comprehensive Yeast Genome Database
- Proteome Analysis
- GenQuiz EBI (UK)
- Proteome analysis @ EBI (UK)
- By organisms, species, groups
- Animals
- AnimalQTLdb (a livestock Quantitative Trait Loci database tool set for positional QTL information mining and beyond) Iowa (USA)
- ARK Database Family (Cat, Chicken, Cow, Deer, Horse, Pig, Sheep ...) Roslin (UK)
- BovMap INRA
- Cat (Felix catus) Ensembl
- Cattle, Swine and Sheep Genomes Maps ARS (USA)
- Cavia porcellus (Guinea Pig) Ensembl
- ChickBASE USDA-CSREES
- ChickVD (a sequence variation database for the chicken genome) Beijing (China)
- Chicken Ensembl
- Chimpanzee Ensembl
- Cow Genome Project Ensembl
- The Canine Radiation Hybrid Mapping Project Rennes (French), see also CRH_Server
- Dasypus novemcinctus Ensembl
- Dog Ensembl EMBL-EBI-Sanger
- Dog Genome Project Berkeley
- Echinops telfairi Ensembl
- Elephant (Loxodonta africana) - Ensembl Sanger-EBI (UK)
- Ensembl (genomic sequence with features attached) EMBL-EBI-Sanger
- Equus caballus PreEnsembl
- Erinaceus europaeus (western European hedgehog) Ensembl
- Fugu Genome Project IMCB
- FUGU Project (Fugu rubripes) HGMP (UK)
- Fugu Ensembl EMBL-EBI-Sanger
- GoSh (database for goat and sheep EST sequences) Lodi (Italie)
- Livestock Genome Mapping Programmes (Bovine, chicken, dog, goat, pig, sheep) INRA (France)
- MamPol (a database of nucleotide polymorphism in the Mammalia class) Barcelona (Spain)
- MIS (Mendelian Inheritance in Sheep) Angis (Australia)
- Myotis lucifugus Ensembl
- Opossum (Monodelphis domestica) Ensembl
- Ornithorhynchus anatinus (Platypus) Ensembl
- Oryctolagus cuniculus (rabbit) Ensembl
- Otolemur_garnettii (Bushbaby) Ensembl
- Pig Gene Mapping NAGRP, see also Roslin (UK)
- PEDE (database for ESTs derived from porcine full-length cDNA libraries) Ibaraki (Japan)
- PigGIS (pig genomic informatics system) Beijing (China)
- Porcine Genome Physical Mapping Project (Sus scrofa) Sanger (UK)
- Rhesus macaque (Macaca mulatta) Ensembl
- Sorex araneus Ensembl
- Spermophilus tridecemlineatus Ensembl
- Sus scrofa (pig) PreEnsembl
- Sus scrofa map Viewer PreEnsembl
- Tupaia belangeri Ensembl
- VEGA (Vertebrate Genome Annotation database) Sanger (UK)
- Arabidopsis
- AAtDB (Harvard) www (USA)
- Arabidopsis Co-expression Tool (ACT) (tools for microarray-based gene expression analysis) Leeds (UK)
- A Complete Arabidopsis Transcriptome MicroArray catma
- Arabidopsis Gene Hunter (searches databases and web sites) TAIR (USA)
- FLAGdb++ (integration and exploration around the Arabidopsis genome) INRA (French)
- Arabidopsis Genomic RNAi Knock-out Line Analysis agrikola
- Arabidopsis Information Resource (Maps, Databases, Tools,..) TAIR (USA)
- Genomic Arabidopsis Resource Network GARNET (UK)
- Arabidopsis data KAOS (Japan)
- Arabidopsis Sequencing at Stanford (USA)
- ASRP (the Arabidopsis Small RNA Project Database) Oregon (USA)
- Athena (resource for rapid visualization and systematic analysis of Arabidopsis promoter sequences) Washington (USA)
- Links to Arabidopsis thaliana WWW sites and to SWISS-PROT entries Expasy
- AthaMap (resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome) Braunschweig (Germany)
- AtNoPDB (Arabidopsis nucleolar protein database) Dundee (Scotland)
- ATTED-II (a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis) Yokohama (Japan)
- Flanking Sequence Tags InfoBioGen (French)
- GABI-Kat (database of flanking sequence tags (FSTs) of T-DNA mutagenized Arabidopsis thaliana) Koeln (Germany)
- GeneFarm (structural and functional annotation of Arabidopsis gene and protein families by a network of experts) INRA (French)
- GeneNest Index (EST Clustering Projects) Heidelberg (Germany)
- Genoscope CNS (France)
- Arabidopsis Beta-glucosidases and galactosidases Iowa (USA)
- Arabidopsis Cytochromes P450 Biobase (Denmark)
- Arabidopsis Cytochrome b5 Biobase (Denmark)
- Arabidopsis Glucosyltransferases Biobase (Denmark)
- Insertion database CSHL (USA)
- Arabidopsis P450 Reductase Biobase (Denmark)
- MATDB (MIPS Arabidopsis thaliana database) MIPS (Germany)
- Arabidopsis Membrane Protein Library CBS (USA)
- AMPDB (the Arabidopsis Mitochondrial Protein Database) Crawley (Australia)
- NASCArrays (a repository for microarray data generated by NASC's transcriptomics service) Nottingham (UK)
- PAT (Proteins of Arabidopsis Thaliana Database) SDSC (USA)
- Arabidopsis Membrane Protein Library CBS (USA)
- Functional genomics of P450 Illinois (USA)
- Mutant Genes Oklahoma (USA)
- PlantQTL-GE (a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information) Shanghai (China)
- RARGE (a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome) Riken (Japan)
- SIGnAL Arabidopsis Gene Mapping Tool SIGAL (USA)
- SpliceN EST Max-Planck (Germany)
- Structural genomics (three-dimensional structure) CESG (USA)
- DATF (database of transcription factors) Beijing (China)
- SUBA (the Arabidopsis Subcellular Database) Crawley (Australia)
- Transposon Tagging PennState (USA)
- The TIGR Arabidopsis thaliana Database ATDb (USA)
- Bacillus
- Bacillus anthracis Porton Ames isolate TIGR (USA)
- Bacillus Subtilis
- Bacillus Subtilis NIST, see also Pasteur
- Bacillus Subtilis 168 TIGR (USA)
- DBTBS (promoters and transcription factors database) Tokyo (Japan)
- MadBase (and BadBase an ACeDB version) INRA (France), see also Micado Main Menu
- A Non-Redundant Database for Bacillus subtilis NRSub (Lyon)
- Bacillus Subtilis : neighbouring genes and codon usage Versailles (France)
- Links to B. subtilis WWW sites and to SWISS-PROT entries Expasy
- Micado (prokaryotes and Bacillus subtilis) INRA (French)
- PEDANT MIPS (Germany)
- SPiD (Protein interaction Database) INRA (French)
- SubtiList Pasteur (French)
- SRS : at DKFZ (Germany)
- C. elegans
- AppaDB (an AcedB database for the nematode satellite organism Pristionchus pacificus) Tuebingen (Germany)
- CEPDB (C. elegans Promoter Database) CSHL (USA)
- Cold Spring Harbor CSHL (USA)
- The Sanger Centre www
- UTSW C. elegans server www (Texas)
- C. elegans Mitochondrial genetics Sanger (UK)
- Links to C. elegans WWW sites and to SWISS-PROT entries Expasy
- Nematode.net (a tool for navigating sequences from parasitic and free-living nematodes) Washington (USA)
- NEMBASE (a resource for parasitic nematode ESTs) Edinburgh (UK)
- NEXTDB (nematode expression pattern database) NIG (Japan)
- RNAi in C. elegans New York (USA)
- RNAi at @elegans (USA)
- SGCEdb (a flexible database and web interface integrating experimental results and analysis for structural genomics focusing on Caenorhabditis elegans) Alabama (USA)
- WormBase California (USA)
- Worm Book (the online review of Caenorhabditis elegans biology) California (USA)
- Human and Nematode Orthologs NCBI (USA)
- Worm-Yeast Protein Comparison Stanford (USA)
- Conidae
- Crayfish
- Ciliated protozoans
- MDS_IES_DB (database of macronuclear and micronuclear genes in spirotrichous ciliates) Princeton (USA)
- TGD (Tetrahymena Genome Database) TIGR-UCSB-Stanford (USA)
- Ciona intestinalis
- DBTGR (a database of tunicate promoters and their regulatory elements) Tokyo (Japan)
- Ensembl Sanger-EBI (UK)
- Ciona savignyi
- DBTGR (a database of tunicate promoters and their regulatory elements) Tokyo (Japan)
- Ensembl Sanger-EBI (UK)
- Diatom
- Dictyostelium
- cDNA Project Tsukuba (Japan)
- DictyDB (Dictyostelium discoideum) San Diego (USA)
- DictyDB (Dictyostelium discoideum) UCSD (USA)
- dictyBase
- Dictyostelium Project BCM (USA)
- Dictyostelium Project Jena (Germany)
- Drosophila
- Atlas of the Drosophila nervous system www (Freiburg)
- DNase I footprint database (a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster) Cambridge (UK)
- Berkeley Drosophila Genome Project BDGP (USA)
- DBSD (Drosophila binding site database) CSHL (USA)
- DroSpeGe (rapid access database for new Drosophila species genomes) Indiana (USA)
- Ensembl (genomic sequence with features attached) Sanger-EBI
- Entrez genome NCBI (USA)
- FLIGHT (database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets) Londres (UK)
- FlyBase (Indiana) www, see also Search (Harvard)
- FlyBase (genes and gene models) Harvard (USA)
- FlyBrain USA (USA)
- FlyEx (database on gene expression in segmentation genetic network) New York (USA)
- FlyMine (integrated database for Drosophila and Anopheles genomics) Cambridge (UK)
- FlyRNAi (the Drosophila RNAi screening center database) Harvard (USA)
- FlyTF (transcription factors database) Cambridge (UK)
- FlyTrap (relational database of transposable element insertions) California (USA)
- FlyView (Muenster) www (image database on Drosophila development), see also FlyMove
- GenomeRNAi (a database for cell-based RNAi phenotypes) Heidelberg (Germany)
- Index of Drosophila entries and their corresponding FlyBase cross-references Expasy
- The Interactive Fly (A cyberspace guide to Drosophila genes and their roles in development) FlyBase (USA)
- MitoDrome (nuclear genes encoding proteins targeted to the mitochondrion) Bari (Italy)
- The Drosophila P450 Site INRA (French)
- REDfly (a regulatory element database for Drosophila) Buffalo (USA)
- SegNet (Segmentation Gene Networks) Russian Network
- SpliceN EST Max-Planck (Germany)
- Wnt genes in Drosophila Stanford (USA)
- SRS - EnsemblPepFruitFly Sanger (UK)
- SRS - FlyGene - FlyPeople - FlyPep - FlyRef DKFZ (Germany)
- Fungi
- Ashbya gossypii Basel (Switzerland)
- Aspergillus fumigatus Genome Project TIGR (USA)
- Aspergillus nidulans MIT (USA)
- Aspergillus oryzae RIB40 NITE (Japan)
- CADRE (the Central Aspergillus Data REpository) Manchester (UK)
- Cryptococcus neoformans TIGR (USA)
- Cryptococcus neoformans Stanford (USA)
- FGSC (Fungal Genetics Stock Center) Kansas (USA)
- Fungal Cosmid and cDNA Sequencing Oklahoma (USA)
- Fungal genomes Sanger (UK)
- Fungal genome databases MIP (Germany)
- Fungal Genome Initiative MIT (USA)
- Fungal genome resource Georgia (USA)
- Fusarium graminearum genome database MIPS (Germany)
- Fusarium sporotrichioides Oklahoma (USA)
- Index of Mycoplasma genitalium strain G-37 chromosomal entries Expasy
- Magnaporthe grisea (FDB) NCSU (USA)
- Mycoplasma genitalium : PEDANT MIPS (Germany)
- Mycoplasma genitalium : Structural Assignments to MG Proteins Yale (USA)
- Mycoplasma pneumoniae M129 DDBJ (Japan)
- Mycoplasma pneumoniae (Sequences, Metabolic Pathways) Heidelberg (Germany), see also Expasy
- Mycoplasma pneumoniae : PEDANT MIPS (Germany)
- Mycoplasma pneumoniae M129 TIGR (USA)
- Mycoplasma pulmonis (MypuList) Pasteur (French)
- Mycor Web (E. globulus - P. tinctorius) INRA (France)
- Neurospora crassa database MIT (USA)
- Neurospora crassa Gene List Leeds (UK)
- Neurospora genome project New Mexico (USA), see also MIPS (Germany)
- Search CBS Filamentous Fungi database CBS (Denmark)
- Ustilago maydis genome database MIPS (Germany)
- Gasterosteus aculeatus
- Human
- 5'SAGE (5'-end Serial Analysis of Gene Expression database) Tokyo (Japan)
- ABS (a database of Annotated regulatory Binding Sites from orthologous promoters) Barcelona (Spain)
- AceView (genes. clones, ESTs) NCBI (USA)
- Alternative Splicing (AS) Berlin (Germany)
- Alternative Splicing Database (ASD) EBI (UK)
- Alternative Splicing Gallery - ASG (bridging the gap between genome and transcriptome) North Carolina (USA)
- Alternative splicing (SpliceInfo) Taoyuan (Taiwan)
- ASHESdb (Alternatively Spliced Human genes by Exon Skipping) Singapore
- AluGene (database of Alu elements incorporated within protein-coding genes) Tel Aviv (Israel)
- CCDS (a core set of human protein-coding regions that are consistently annotated and of high quality) NCBI (USA)
- cisRED (a database system for genome-scale computational discovery of regulatory elements) Vancouver (Canada)
- Copy Number Variation (CNV) Project Sanger (UK)
- D-HaploDB (a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples) Fukuoka (Japan)
- ECgene (Gene Modelling with Alternative Splicing) Seoul (Korea)
- ENCODE project California, see also NHGRI (USA), see also Sanger, see also ENCODE regions in Vega Sanger
- Ensembl, see also Encode
- ExoSeq (search for sequence variation in the human genome) Sanger (UK)
- FINDbase (a relational database recording frequencies of genetic defects leading to inherited disorders worldwide) Montreal (Canada)
- GDB and OMIM GenomeNet (Japan) www (DBGET)
- GDB et OMIM (John Hopkins) www (Search by Keyword, Name, Gene name, Map location ...), mirror list
- GDB and OMIM WEHI (Australia)
- GDB and OMIM Weizman (Israel)
- GENATLAS (genes, diseases, and markers) Paris (France)
- GENEVAR (gene expression variation) Sanger (UK)
- Genew (the Human Gene Nomenclature Database) London (UK)
- HAGR (the Human Ageing Genomic Resources) Boston (USA)
- HIB : database of annotated UniGene clusters MIPS (Germany)
- H-InvDB (integrated database of human transcriptome) BIRC (Japan)
- HOLLYWOOD (a comparative relational database of alternative splicing) MIT (USA)
- HOWDY (integrated database) Tokyo (Japan)
- HPI (Human Proteomics Initiative) Expasy
- HPRD (human protein reference database as a discovery resource for proteomics) HPRD
- HUGE (Human Unidentified Gene-Encoded Large Proteins) Kazusa (Japan)
- HugeIndex ZLab (USA)
- Human fusion proteins Singapore
- International Protein Index (IPI : human, mouse proteomes) EMBL-EBI (UK)
- LocusLink (NCBI RefSeq : a non-redundant set of reference sequences, including constructed genomic contigs, mRNAs, proteins) NCBI (USA)
- MITOMAP (mitochondrial genome database) California (USA)
- OMIM NCBI (USA), search
- Protein Atlas Stockholm (Sweden)
- STACK (Sequence Tag Alignment and Consensus Knowledgebase) SANBI (South Africa)
- STRBase (Short Tandem Repeat DNA) NIST (USA)
- TIGR Expressed Gene Anatomy Database EGAD (USA)
- TIGR Human Gene Index HGI (USA)
- Unique Human Gene Sequence Collection (Search and list by chromosome) UniGene (NCBI : USA), see also : alignment ProtEST
- CEPH (Généthon) www (Physical Map, YAC), see also
- CHLC (Cooperative Human Linkage Center) NCI (USA)
- Center for Medical Genetics (genetics maps, markers, CEPH..) CMG (USA)
- GenLink (GenotypesDB, TelDB, Meiotic Maps) WU (USA)
- A Gene Map of the Human Genome (Transcript map : Science 96) NCBI (USA)
- Gene Map NCBI (USA)
- Genome Browser UCSC, another link (USA)
- Genome Map 98 EBI, Map 99 (UK)
- Genome map viewer NCBI (USA), see also Tour Human
- GeneNest Index (EST Clustering Projects) Max-Planck (Germany)
- Human BAC Mapping Data MIT (USA)
- Human Gene Nomenclature Database Search UCL (UK)
- Human Genome Guide NCBI (USA)
- Human Genome Project (Chromosome, RHT, EST, Polymorphism) Sanger (UK)
- Human Genome Sequencing NCBI (USA)
- BCMGC (Houston) www
- HPID (Human protein interaction database) Daejeon (Korea)
- LDB2000 (Sequence-based Integrated Maps of the Human Genome) Southampton, see also LDB (UK)
- qPrimerDepot (a primer database for quantitative real time PCR) Baltimore (USA)
- SHGC center (Mapping, Sequencing, RH server) Stanford (USA)
- Human Genome Project Working Draft UCSC (USA)
- T-STAG (tissue-specific transcripts and genes) Berlin (Germany)
- UniHI (an entry gate to the human protein interactome) Berlin (Germany)
- SRS - OMIM (linked libraries : OMIM) : almost all the [SRS] servers
- SRS - CPGISLE (linked libraries : CPGISLE Human CpG-island database) DKFZ (Germany)
- SRS - MIMMAP (linked or genomic libraries : MIMMAP) DFKZ (Germany)
- SRS - EnsemblCdna_Human - EnsemblPep_Human : Sanger (UK)
- SRS - Human_Ensembl - Human_Ensembl_CDNA - Human_Ensembl_Prot - Human_Ensembl_RNA : DFKZ (Germany)
- SRS - Human_Isochores - Human_Locus - Human_MGC - Human_mRNA - Human_Prot : DFKZ (Germany)
- SRS - RHXX (mapping libraries : RHDB, RHEXP, RHPANEL) : à DKFZ (Germany)
- SRS - UNIGENE : almost all the [SRS] servers
- SRS - VIRGIL : at DKFZ (Germany), WEHI (Australia)
- Chromosomes
- Chromosome Launchpad ORNL (USA)
- Chromosomes 1-22, X, Y UniGene (NCBI : USA), see also HUGO
- Chromosomes 1, 6, 9, 10, 13, 20, 22, X Sanger (UK)
- Chromosomes 1, 9, 11, 22 Oklahoma (USA)
- Chromosomes 5, 16, 19 JGI (USA)
- Chromosome 1 Rockefeller (USA), see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 2 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 3 UTHSCSA, see also Baylor (USA), see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 4 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 5 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 6 Sanger (UK), see also GHR, see also Protein sequence entries in SwissProt Expasy, see also MHC Haplotype Project Sanger
- Chromosome 7 NHGRI (USA), see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 8 UTHSCSA, see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 9 Cambridge see also report on 3rd International Chromosome 9 Workshop, see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 10 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 11 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 12 Baylor, see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 13 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 14 Genoscope, see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 15 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 16 TIGR (USA), see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 17 GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 18 GHR,see also Protein sequence entries in SwissProt Expasy
- Chromosome 19 LLNL see also DNA Repair (California), see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 20 Sanger (UK), see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 21 CEPH (France), see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome 22 Sanger centre (UK), see also GAIA 22, see also GHR, see also Protein sequence entries in SwissProt Expasy, see also GALA (Genome Alignment and Annotation Database) Pennsylvania
- Chromosome X Max Planck (Deuchtland), see also Baylor, see also GHR, see also Protein sequence entries in SwissProt Expasy
- Chromosome X : IXDB (integrated database) Berlin (Germany), see also MPI
- Chromosome Y GHR, see also Protein sequence entries in SwissProt Expasy
- Human-Mouse Homology chromosome regions and genes Softberry (USA)
- Chromosome Abnormality Database Oxford (UK)
- Human Chromosome Aberration database (HCAD) Madrid (Spain)
- Chromosomal breakpoints in human cancer NCBI (USA)
- MITOMAP: A database of the "Report of the committee on human mitochondrial DNA" Emory (Georgia)
- Cytogenetics Gallery Washington (USA)
- ABC transporters Wageningen (The Netherlands)
- ALFRED (Allele Frequency Database) Yale (USA)
- ALPSbase (Autoimmune Lymphoproliferative Syndrome) NHGRI (USA)
- APDD (the Archaeal Pathogen Detection Database) Sydney (Australia)
- ARED (AU rich element containing mRNA database) Riyadh (Saudi Arabia)
- Atlas of Genetics and Cytogenetics in Oncology and Haematology Poitiers (French)
- Blood Group Antigen Gene Mutation Database NCBIBodyMap (Anatomical Expression Database of Human Genes) IMCB (Japan)
- BreastDB - Breast cancer drug resistance screen Database NCI (USA)
- The Cancer Genome Anatomy Project (CGAP) NCBI (USA)
- CancerGenes (a gene selection resource for cancer genome projects) New York (USA)
- Cancer gene expression database (CGED) Osaka (Japan)
- Cancer genome project Sanger (UK)
- CARGO (portal to integrate customized biological information) Madrid (Spain)
- Connexin-deafness IRO (Spain)
- COSMIC (somatic mutations in cancer) Sanger (UK)
- Database of Chromosome Aberrations in Cancer (Mitelman) NCI (USA)
- DG-CST (Disease Gene Conserved Sequence Tags, a database of human-mouse conserved elements associated to disease genes) Naples (Italy)
- Diabetes (T1D, type 1) Cambridge (UK)
- Entrez : Cancer Chromosomes NCBI (USA)
- EPConDB (resource for gene expression related to pancreatic development, beta-cell function and diabetes) Pennsylvania (USA)
- Factor VII mutation db London (UK)
- G2D (candidate genes for mapped inherited human diseases) EMBL (Germany), see also Ottawa (Canada)
- GeneCards (functions of genes and their products) Weizmann, mirror sites
- GeneCards : GeneTide (Terra Incognita Discovery Endeavor) Weizmann (Israel)
- GENDIAG (Genetic Syndromes and Abnormalities in Development in Man - Orphanet) Paris (French)
- GeneDis (Human Genetic Disease Database) Tel Aviv (Israel)
- Genes and Diseases NCBI (USA), another link
- Genetic Disorders by Chromosome GDB (USA)
- GeneTrap (modeling human disease gene trap resource) Toronto (Canada)
- H-ANGEL (Human Anatomic Gene Expression Library) Tokyo (Japan)
- HapMap (expected to be a key resource for researchers to use to find genes affecting health, disease, and responses to drugs and environmental factors) IHMP
- H-DBAS (Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational) Tokyo (Japan)
- Hembase (human erythroid transcriptome database) Rockville Pike (USA)
- Hera (human endoplasmic reticulum resident proteins database) Montreal (Canada)
- HERVd (human endogenous retroviruses) Prague (Czech Republic)
- HIV1 - Human protein interaction database NIAID (USA)
- HPtaa (database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma) Beijing (China)
- Human Epigenome Project (aims to identify and catalogue Methylation Variable Positions (MVPs)) Sanger (UK)
- Human Genome Variation Database (HGVBASE) CGR (Sweden)
- Human Hexosaminidase A mutation db (Tay-sachs disease) Tel Aviv (Israel)
- Human Short Insertion Deletion Polymorphisms CMG (USA)
- Human and Mouse Transcribed Sequences (DOTS) CBIL (USA)
- Human Full Length cDNA Database KDRI (Japan)
- KBERG (knowledgebase for estrogen responsive genes) Singapore
- L1Base (database containing putatively active LINE-1) Max-Planck (Germany)
- Human leukemia cell lines proteome Paris13 (French)
- OncoDB.HCC (an integrated oncogenomic database of hepatocellular carcinoma revealed aberrant cancer target genes and loci) Taipei (Taiwan)
- Phenylalanine hydroxylase (PAH) mutation db McGill (Canada)
- PolyDoms (a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease) Cincinnati (USA)
- QTL (a multi-species quantitative trait loci database) New York (USA)
- Retinoblastoma-associated protein (RB) mutation db Lohmann (Germany)
- Human Plasma Membrane Receptome (HPMR) Stanford (USA)
- Human proteins with sequence variants Expasy
- Human STS vs YAC Screening Database MIT (USA)
- Human Radiation Hybrid (RHdb) EBI
- Human Radiation Hybrid Mapping Sanger (UK), see also EBI (UK)
- Human Repetitive Elements NCBI (USA)
- HuSiDa (the human siRNA database) Berlin (Germany)
- SKY and CGH Database (Spectral Karyotyping (SKY) and Comparative Genomic Hybidization (CGH)) NCBI (USA)
- Glovar (genomic variation database) Sanger (UK)
- Human SNP (database of single nucleotide polymorphisms) NCBI, see also MIT, see also UW-FHCRC
- FASTSNP (an always up-to-date and extendable service for SNP function analysis and prioritization) Taipei (Taiwan)
- FESD (a Functional Element SNPs Database in human) Seoul (Korea)
- Human PicSNP (Non-Synonymous SNP) UMIN (Japan)
- SAAP (single amino acid polymorphism) London (UK)
- Snap (an integrated SNP annotation platform) Aarhus (Denmark)
- SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms Daejeon (Korea)
- SNP allele frequencies Chicago (USA)
- SNP2NMD (database of human single nucleotide polymorphisms causing nonsense-mediated mRNA decay) Dajeon (Korea)
- SNPs in the Context of Transcripts, ORFs and Protein Motifs (Gene Viewer) NCI (USA)
- topoSNP (a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association) Illinois (USA)
- SNPeffect (a database mapping molecular phenotypic effects of human non-synonymous coding SNPs) Brussels (Belgium)
- SNP Function Portal (database for exploring the function implication of SNP alleles) Michigan (USA)
- SNPtoGO (characterizing SNPs by enriched GO terms) Magdeburg (Germany)
- PupasView (tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes) Barcelona (Spain)
- SNP500Cancer (a public resource for sequence validation and assay development for genetic variation in candidate genes) NCI (USA)
- SynDB (a synapse protein database based on synapse ontology) Beijing (China)
- Human Transcript Database Baylor (USA)
- dbGaP (Genotype and Phenotype - to elucidate the link between genes and disease) NCBI (USA)
- EGAD - The Expressed Gene Anatomy Database TIGR (USA)
- EICO (finding disease-related imprinted genes) Riken (Japan)
- GeneSeeker (extraction and integration of human disease-related information from web-based genetic databases) Nijmegen (The Netherlands)
- HbVar (Human Hemoglobin Variants and Thalassemias) Pennsylvania (USA)
- HESAS (HERVs Expression and Structure Analysis System) Busan (Korea)
- HMDB (the Human metabolome database) Edmonton (Canada)
- LDB - The genetic Location Database Southampton (UK)
- LOH (loss of heterozygosity maps from over 800 cancer cell lines and normal samples) Sanger (UK)
- The Human Gene Mutation Database Cardiff (PMDB : Point Mutation DB, MDDB : Micro-Deletion DB)
- HUMHOT (human meiotic recombination hot spots) Bangalore (India)
- IL2RGbase (Database of Mutations Causing Human X-Linked SCID) NHGRI-NIH (USA)
- Immunodeficiency Mutation Databases Helsinki (Finland)
- IPD (Immuno Polymorphism Database) EBI (UK)
- ITTACA (database for integrated tumor transcriptome array and clinical data analysis) Institut Curie (French)
- KMDB/MutationView (Blood, Brain, Cancer, Ear, Eye, Heart, Muscle, autoimune)Keio (Japan)
- Lowe Syndrome Mutation Database (OCRL1 gene) NHGRI (USA)
- MHC database (DNA and clinical data) NCBI (USA)
- MitoP2 (the mitochondrial proteome database - yeast, mouse, human) Munich (Germany)
- mtDB (human mitochondrial genome database, a resource for population genetics and medical sciences) Uppsala (Sweden)
- Mutation registry for X-linked agammaglobulinemia BTKbase (Finland)
- MutDB Indiana (USA)
- NCL mutations (Neuronal Ceroid Lipofuscinoses) UCL (UK)
- NDDs (commonality of protein interaction networks determined in neurodegenerative disorders) Kyoto (Japan)
- Neuropathology Atlas HNM (Hungary)
- OPHID (online predicted human interaction database) Toronto (Canada)
- PolymiRTS (linking polymorphisms in microRNA target sites with complex traits) Tennessee (USA)
- PRIDE (a public repository of protein and peptide identifications for the proteomics community) EBI (UK)
- RNAi (small inhibitory RNAs against human and mouse genes) MIT (USA)
- RNAi codex (a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs) CSHL (USA)
- SCAdb (spinocerebellar ataxia candidate gene database) Taiwan (Republic of China)
- SIEGE (Smoking Induced Epithelial Gene Expression) Boston (USA)
- Somatic p53 mutations in human tumors and cell lines IARC (France)
- SpliceN EST Max-Planck (Germany)
- EASED (Extended Alternatively Spliced EST Database) Berlin (Germany)
- TiProD (tissue-specific promoter database) Beijing (China)
- TRbase (a database relating tandem repeats to disease genes for the human genome) Exeter (UK)
- UMD (Universal mutation database : APC, FBN1, LDLR, MEN1, p53, SUR1, VHL, WT1) Montpellier (French)
- VBASE2 (germ-line sequences of human and mouse immunoglobulin variable (V) genes) Braunschweig (Germany), another link
- VISTA Enhancer Browser (a database of tissue-specific human enhancers) Berkeley (USA)
- VMD2 Mutation Database Wurzburg (Germany)
- von Willebrand factor (vWF) mutation db Sheffield (UK)
- WRN mutation db (Werner disease) Washington (USA)
- X-ALD gene mutation database Amsterdam (Netherlands)
- The Whole Brain Atlas Harvard (clinical information with magnetic resonance (MR), x-ray computed tomography)
- VectorBase (a home for invertebrate vectors of human pathogens) London (UK)
- Homophila (human disease to drosophila genes) SDSC (USA)
- GenomeTrafac (a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs) Cincinnati (USA)
- Godzilla (Compare the Human and Mouse Genomes) Berkeley (USA)
- Human/Mouse Homology Relationships NCBI (USA)
- Human-Mouse Gene Searcher (a tool to assist discovery of malformation-associated genes by using phenotype databases) London (UK)
- SLAM (submit pairs of syntenic sequences for gene annotation and alignment) Berkeley (USA)
- Whole Genome Human/Mouse Homology Penn State (USA)
- Human and Nematode Orthologs NCBI (USA)
- Insect
- AphidBase (database for aphid genomic resources) INRA (France)
- InSatDb (a microsatellite database of fully sequenced insect genomes) Hyderabad (India)
- BeetleBase (the model organism database for Tribolium castaneum) Kansas (USA)
- Fulgoromorpha Jussieu (French)
- Honeybee Ensembl
- Medakafish
- MBase (ME - expressed sequence tag, ML - linkage map, MB - BAC) Tokyo (Japan)
- Medaka genome project NIG (Japan)
- Ensembl
- MEPD (Medaka expression pattern database) EMBL (Germany)
- UTGB Tokyo (Japan)
- WWW server of the Medakafish Nagoya (Japan)
- Mosquitos
- Mouse
- ABS (a database of Annotated regulatory Binding Sites from orthologous promoters) Barcelona (Spain)
- Anatomical Dictionary Browser Jackson Lab (USA)
- ARTS (a tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants) Neuherberg (Germany)
- Alternative Splicing Database (ASD) EBI (UK)
- Atlas Project (Genex) MRC (UK)
- ChimerDB Seoul (Korea)
- Chromosomes
- Cytogenetic Map Image NIAI (Japan)
- ECgene (Gene Modelling with Alternative Splicing) Seoul (Korea)
- EICO (finding disease-related imprinted genes) Riken (Japan)
- EMAGE (a spatial database of gene expression patterns during mouse embryo development) Edinburgh (UK)
- FANTOM (functional annotation of mouse) Riken (Japan)
- FREP Database (Functional Repeats in Mouse cDNAs) Riken (Japan)
- GeneNest Index (EST Clustering Projects) Max-Planck (Germany)
- GenePaint (an atlas of gene expression patterns in the mouse embryo) Max Planck Institute (Germany)
- Genetic Map (MIT) www, another link (USA)
- GENSAT (map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques) NCBI (USA)
- GeneTrap (modeling human disease gene trap resource) Toronto (Canada)
- HOLLYWOOD (a comparative relational database of alternative splicing) MIT (USA)
- International Gene Trap Consortium Website (a portal to all publicly available gene trap cell lines in mouse) California
- International Protein Index (IPI : human, mouse proteomes) EMBL-EBI (UK)
- L1Base (database containing putatively active LINE-1) Max-Planck (Germany)
- LOCATE (a mouse protein subcellular localization database) Queensland (Australia)
- Portable Dictionary of the Mouse Genome (University of Tenessee) Nevernet
- Ensembl (genomic sequence with features attached) Sanger-EBI, see also Pre.Ensembl
- Genome - MGD (Jackson Laboratory) www, see also Wehi (Australia)
- MfunGD (annotated mouse genes, proteins and their occurrence in protein networks) MIPS (Germany)
- MGD entries in Swiss-Prot Expasy (Switzerland)
- MICER (Mutagenic Insertion and Chromosome Engineering Resource) Sanger (UK)
- Mouse cDNA project NIA-NIH (USA)
- Mouse Phenome Database (a collection of phenotypic and genotypic data) Jackson Lab (USA)
- Mouse RH Map MIT (USA)
- Pathbase (European database of mutant mouse pathology) EMMPD
- QTL (a multi-species quantitative trait loci database) New York (USA)
- Rat Brain Atlas Project GWER (Switzerland)
- Rat EST Project Iowa (USA)
- Rat Genome Database (RGD) MCW (USA)
- Rat Genome Resources NCBI (USA)
- Rat Map WWW Server Goteborg
- Rattus norvegicus genome view NCBI (USA)
- READ (Riken Expression Array Database) Riken (Japan)
- RNAi (small inhibitory RNAs against human and mouse genes) MIT (USA)
- RTCGD (mouse retroviral tagged cancer gene database) NCIFCRF (USA)
- SAGE (public libraries generated by the Serial Analysis of Gene Expression) Prague (Czech Republic)
- StemCellDatabase (SCDb) Princeton (USA)
- SIGTR (Sanger Institute Gene Trap Resource) Sanger (UK)
- SNPs in the Context of Transcripts, ORFs and Protein Motifs (Gene Viewer) NCI (USA)
- SpliceN EST Max-Planck (Germany)
- TIGR Mouse Gene Index MGI (USA)
- T-STAG (tissue-specific transcripts and genes) Berlin (Germany)
- Trans-NIH mouse initiatives NIH (USA)
- Unique Mouse Sequence Collection UniGene (NCBI : USA), see also rat
- VBASE2 (germ-line sequences of human and mouse immunoglobulin variable (V) genes) Braunschweig (Germany), another link
- Transgenic Mutation (TBASE) Jackson Lab (USA)
- Cytogenetic Correspondence in the Linkage Map (Huamn, Pig, Cattle, Sheep, Rat) NIAI (Japan)
- DG-CST (Disease Gene Conserved Sequence Tags, a database of human-mouse conserved elements associated to disease genes) Naples (Italy)
- The Gene Expression Database (GXD) Jackson, search form (USA)
- Mouse Tumour Biology Data Base (MTD) Jackson (USA)
- Gene Knockouts Database www (mouse phenotypes rendered by the knockout of various molecules) (USA)
- Godzilla (Compare the Human and Mouse Genomes) Berkeley (USA)
- Human and Mouse Transcribed Sequences (DOTS) CBIL (USA)
- Human/Mouse Homology Relationships NCBI (USA)
- SLAM (submit pairs of syntenic sequences for gene annotation and alignment) Berkeley (USA)
- Whole Genome Human/Mouse Homology Penn State (USA)
- Mutant Mouse Database ORNL (USA)
- SKY and CGH Database (Spectral Karyotyping (SKY) and Comparative Genomic Hybidization (CGH)) NCBI (USA)
- ARB Rat Genetic Database (Arthritis and Musculoskeletal and Skin Diseases) NIH (USA)
- Nematostella vectensis
- Paramecium tetraurelia
- ParameciumDB (a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data) Gif-sur-Yvette (France)
- Parasites
- Comparasite (a database for comparative study of transcriptomes of parasites defined by full-length cDNAs : plasmodium, Toxoplasma, Cryptosporidium, Echinococcus) Tokyo (Japan)
- CryptoDB (the Cryptosporidium genome resource) Georgia (USA)
- Filarial Genome Network NIAID-NIH (USA), mirror at ED (UK)
- Kinetoplast Minicircle Sequence Database EBI (UK)
- Leishmania Genome Network EBI (UK)
- Leishmania Project Sanger (UK)
- Malaria Database Melbourne (Australia)
- Malaria Genetics Section NCBI (USA)
- Malaria Genome Project Sanger (UK), see also Stanford (USA)
- Full-Malaria (an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species) Tokyo (Japan)
- Malaria Metabolic Pathway Jerusalem (Israel)
- Parasite-genome (Sequences, Codon Usage, ESTs) EBI (UK), see also Internet Resources and Contacts
- Parasite Databases of Clustered ESTs CBIL (USA), see also ApiESTDB
- Parasite-genome EBI (UK)
- Parasites proteome analysis EBI (UK)
- Plasmodium falciparum Florida (USA)
- Plasmodium falciparum (PlasmoDB) UPENN (USA), another link
- Theileria annulata GeneDB Sanger (UK)
- Toxoplasma gondii ToxoDB
- Trypanosoma brucei Sanger (UK)
- Trypanosoma cruzi Pasteur (French), see also Genome Initiative DDBM (Brasil)
- Plants
- AceDB CropNet (UK)
- Eclat (support vector machines for separation of mixed plant-pathogen EST collections based on codon usage) MIPS (Germany)
- Angiosperm DNA C-Values Database RBG (UK)
- BarleyBase (an expression profiling database for plant genomics) Iowa (USA)
- BeanGenes Database (USA)
- BeanRef CNR (Italy)
- BASC (an integrated bioinformatics system for Brassica research) Victoria (Australia)
- Brassica UK CropNet (UK)
- Brassica ASTRA (an integrated database for Brassica genomic research) Victoria (Australia)
- ChloroplastDB (the Chloroplast Genome Database) Pennsylvania (USA)
- CoffeeDNA Trieste (Italy)
- Cotton DB USDA
- CR-EST (a resource for crop ESTs) Gatersleben (Germany)
- CSRDB (a small RNA integrated database and browser resource for cereals) California (USA)
- Dendrome (Forest tree database) California (USA)
- DPTF (database of poplar transcription factors) Beijing (China)
- DPVweb (a comprehensive database of plant and fungal virus genes and genomes) Herts (UK)
- DRASTIC-INSIGHTS (querying information in a plant gene expression database) Dundee (Scotland)
- Erwinia carotovora (plant pathogen) Sanger (UK)
- ForestTreeDB (a database dedicated to the mining of tree transcriptomes) Laval (Canada)
- GrainGenes (Small grains and Sugarcane) INRA (French)
- GRAMENE (a resource of cereal genomes) Cornell (USA)
- Legume Information System : LIS (an integrated information resource for comparative legume biology) Iowa (USA)
- Maize Database TIGR (USA)
- MaizeGDB (the community database for maize genetics and genomics) Iowa (USA)
- Maize Gene Discovery, DNA Sequencing and Phenotypic Analysis Stanford (USA)
- Maize Mapping Project Missouri (USA)
- MIPSPlantsDB (plant database resource for integrative and comparative plant genome research) Neuherberg (Germany)
- Panzea (database and resource for molecular and functional diversity in the maize genome) Ithaca (USA)
- ncRNAs (noncoding RNAs in plants) Michigan (USA)
- openSputnik (a database to ESTablish comparative plant genomics using unsaturated sequence collections) Turku (Finland)
- PathoPlant (a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses) Braunschweig (Germany)
- Phytome (a platform for plant comparative genomics) North Carolina (USA)
- PhytoProt (a database of clusters of plant proteins) Genoplante (French)
- PLACE (cis-acting regulatory DNA elements db) DISC (Japan)
- PlantCARE (cis-acting regulatory element database) Gent (Belgium)
- PlantGDB (plant genome database and analysis tools) Iowa (USA)
- Plant Genetics and Genomics platform Victoria (Australia)
- PlantMarkers (a database of predicted molecular markers from plants) Turku (Finland)
- Plant MPSS databases (signature-based transcriptional resources for analyses of mRNA and small RNA) Delaware Newark (USA)
- PlantProm DB (promoter sequences) London (UK)
- Plant Repeat Databases TIGR (USA)
- PlantSat (Plant satellite DNA) IPMB (Czech Republic)
- Plant snoRNA Database (small nucleolar RNAs) SCRI (UK)
- Plant Transcript Assemblies database TIGR (USA)
- PLMItRNA/SRS (mitochondrial tRNAs and tRNA genes) Bari (Italy)
- POGs/PlantRBP (a resource for comparative genomics in plants) Oregon (USA)
- PoMaMo (a comprehensive database for potato genome data) Cologne (Germany)
- BGI-RIS (an integrated information resource and comparative analysis workbench for rice genomics) Beijing (China)
- RAP-DB (hub for Oryza sativa ssp. japonica genome information) Tokyo (Japan)
- RetrOryza (a database of the rice LTR-retrotransposons) Perpignan (French)
- Rice Annotation Database (RAD) (a contig-oriented database for map-based rice genomics) Ibaraki (Japan)
- PlantQTL-GE (a database system for identifying candidate genes in rice and Arabidopsis by gene expression and QTL information) Shanghai (China)
- Rice Genome Project Wisconsin (USA)
- Rice Genome Research AFFRC (Japan)
- Rice Knowledge Bank IRRI (USA)
- OryGenesDB (an interactive tool for Rice reverse genetics) CIRAD (French)
- Rice Pipeline (a unification tool for plant functional genomics) Ibaraki (Japan)
- Rice Proteome Database based on two-dimensional polyacrylamide gel electrophoresis Tokyo (Japan)
- Rice-research Monsanto (USA)
- Rice Transcription Factors (DRTF) Beijing (China)
- SGN comparative map viewer (sol genomics network) Cornell (USA)
- RMD (a rice mutant database for functional analysis of the rice genome) Wuhan (China)
- Solanaceae Genomics Project Cornell (USA)
- Sorghum bicolor Texas (USA)
- TIGR Rice Gene Index OGI (USA), see also Rice genome
- SoyBase Iowa (USA)
- SoyGD (a browser for display of duplicated, polyploid, regions and sequence tagged sites on the integrated physical and genetic maps of Glycine max) Illinois (USA)
- SGMB (Soybean genomics and microarray database) USDA-ARS (USA)
- TED (tomato expression database) Cornell (USA)
- TomatEST database (in silico exploitation of EST data to explore expression patterns in tomato species) Naples (Italy)
- TropGENE (database of tropical crops) Cirad (French)
- Wheat Estimated Transcript Server (WhETS) (a tool to provide best estimate of hexaploid wheat transcript sequence) Hertfordshire (UK)
- Prokaryotes
- List of Bacterial Names with Standing in Nomenclature Euzeby (French)
- Archaeal Genome Browser California (USA)
- BacMap (an interactive picture atlas of annotated bacterial genomes) Alberta (Canada)
- BacTregulators (database of transcriptional regulators in bacteria and archaea) Granada (Spain)
- BAGET (server for the effortless retrieval of prokaryotic gene context and sequence) Orsay (French)
- BIBI (Bio informatic bacterial identification) PBIL (French)
- EnteriX (Visualization Tools for Bacterial Genome Alignments) PensylvaniaFusionDB (database for in-depth analysis of prokaryotic gene fusion events) IGS (French)
- GeConT (gene context analysis) Morelos (Mexico)
- GeneTrees (a phylogenomics resource for prokaryotes) Virginia (USA)
- Genome Properties (a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics) TIGR (USA)
- ICDS (interrupted CoDing sequences in prokaryotic genomes) Strasbourg (French)
- IMG (integrated microbial genomes system) DEJGI (USA)
- ISfinder (centre for bacterial insertion sequences) Toulouse (French)
- Islander (Prophages Incorporated into Bacterial Genomes) Indiana (USA)
- IslandPath (aiding detection of genomic islands in prokaryotes) Burnaby (Canada)
- MICdb (Prokaryotic Microsatellites Database) Hyderabad (India)
- MiST (a microbial signal transduction database) Tennessee (USA)
- MvirDB (a microbial database of protein toxins, virulence factors and antibiotic resistance genes for bio-defence applications) LLNL (USA)
- ORF and sequences retriever U-ParisSud (French)
- ORFan database Beer-Sheva (Israel)
- Phydbac (display phylogenomic profiles of bacterial protein sequences) IGS (French)
- PRODORIC (prokaryotic database of gene regulation) Braunschweig (Germany)
- PSORTdb (database of protein subcellular localizations for bacteria) Burnaby (Canada)
- Bacterial Nomenclature up-to-date DSMZ (Germany)
- Bacterial Polysaccharide Gene Database Sydney (Australia)
- Bacterial Quorum Sensing Nottingham (UK)
- Bacteroides fragilis (NCTC9343) Sanger (UK)
- VFDB (database for bacterial virulence factors) Beijing (China)
- VNTRDB (a bacterial variable number tandem repeat locus database) Taipei (Taiwan)
- TRACTOR_DB (database of regulatory networks in gamma-proteobacterial genomes) Habana (Cuba)
- Micado (prokaryotes and Bacillus subtilis) INRA (French)
- Microbial Genome Database for Comparative Analysis MBGD (Japan)
- Microbial Genomes at Sanger (UK)
- Microbial Genomes at JGI (USA)
- Microbial Genome Viewer Nijmegen (The Netherlands)
- Mosaic (relational database to compare closely related bacterial genomes) INRA (French)
- Multi Locus Sequence Typing MLST
- Genomic Threading London (UK)
- Homologous Bacterial Genes Database PBIL (France)
- PGTdb (Prokaryotic Growth Temperature Database) DLS (Taiwan)
- RegTransBase (database of regulatory sequences and interactions in a wide range of prokaryotic genomes) Berkeley (USA)
- SEEBUGS Microbial Genome Analysis (Concordance, Subtraction, Cluster, Neighbors) Rutgers (USA)
- VIS-O-BAC (exploratory visualization of functional genome studies from bacteria) Braunschweig (Germany)
- Aeropyrum pernix K1 NITE (Japan)
- ARCHAIC (Pyrococcus sp. OT3, Thermoplasma volcanium GSS1, Archaeoglobus fulgidus) AIST (Japan)
- Archaeoglobus fulgidus TIGR (USA)
- Bacteroides Carolina (USA)
- Borrelia burgdorferi (Strain list and Genetic and Physical maps) Pasteur, see also TIGR (USA)
- Bordetella (parapertussis, bronchiseptica, pertussis) Sanger (UK)
- Buchnera iBGD (Japon), see also Expasy
- BuchneraBASE (a post-genomic resource for Buchnera) York (USA)
- CMR Genomes (Comprehensive microbial resource) TIGR (USA)
- Chlamydia GP TIGR (USA)
- Chlamydia Sequencing at Stanford (USA)
- Chromobacterium violaceum VIGR (Brasil)
- Corynebacterium efficiens NITE (Japan)
- Berkeley E. coli Microarray Entry Point Berkeley (USA)
- CCDB (a comprehensive, self-updating, relational database to coordinate and facilitate in silico modeling of Escherichia coli) Alberta (Canada)
- Coli Base Birmingham (UK)
- Colibri World-Wide Web Server Pasteur (French)
- Cowdria ruminantium (Ehrlichia ruminantium) Sanger (UK)
- EchoBASE (an integrated post-genomic database for Escherichia coli) York (USA)
- Ecce (E. Coli cell envelope protein data collection) Cardiff (UK)
- EcoCyc (Encyclopedia of E. coli Genes and Metabolism) Pangea (USA)
- EcoGene Miami (USA)
- Escherichia Coli : PEDANT MIPS (Germany)
- Escherichia Coli : RegulonDB (transcriptional regulation) Morelos (Mexico)
- E. Coli : neighbouring genes and codon usage Versailles (France)
- Escherichia Coli (Yale) www (stock)
- E.coli database collection (ECDC) Giessen (Germany)
- DNA-Proteins interactions db (DPInteract) Harvard (USA)
- E. coli DNA-Binding Site Matrices Harvard (USA)
- E.coli in-frame gene deletion Harvard (USA)
- GenProtEC (Genome and proteome database) MBL (USA)
- HAMAP (High quality Automated Microbial Annotation of Proteomes) Expasy (Switzerland), see also : list of organisms which are currently target of the HAMAP
- Index of Escherichia coli Gene-protein database (ECO2DBASE) entries referenced in SWISS-PROT Expasy
- Links to E.coli WWW sites and to SWISS-PROT entries Expasy
- IS db (insertion sequences isolated from eubacteria and archae) IBCG-LMGM (French)
- MaGe (microbial genome annotation system) Genoscope (French)
- Promec (E. coli mRNA promoters with experimentally identified transcriptional start sites) Jerusalem (Israel)
- SRS - ECDC (linked libraries : ECDC) : DKFZ (Germany)
- SRS - ECDCONTIG (linked libraries : ECDCONTIG) : DKFZ (Germany)
- SRS - ECOLI (linked libraries : ECOLI) : DKFZ (Germany)
- CyanoBase KDRI (Japan)
- CyanoSite Purdue (USA)
- Erwinia carotovora (plant pathogen) Sanger (UK)
- Extremophiles Paris (French)
- Francisella tularensis Uppsala (Sweden)
- Haemophilus influenzae
- FLAN (for influenza virus genome annotation) NCBI (USA)
- Flu Dataset Explorer NCBI (USA)
- FluGenome (for genotyping influenza A virus) Atlanta (USA)
- Influenza Bibliography NIMRC (UK)
- GeneQuiz: automated analysis of Haemophilus influenzae proteins EBI
- Influenza Sequence Database LANL (USA)
- Index of Haemophilus influenzae RD chromosomal entries and gene names with links to the TIGR and EMBL servers Expasy
- The Haemophilus influenzae Rd Genome Database TIGR (USA)
- Influenza Sequence Database LANL (USA)
- Influenza Virus Resource NCBI (USA)
- IVDB (an integrated information resource and analysis platform for influenza virus research) Beijing (China)
- PEDANT MIPS (Germany)
- Halophile genomes Maryland (USA)
- Helicobacter pylori strain 26695 chromosomal entries Expasy
- Helicobacter pylori Genome Database (HPDB) TIGR (USA), see also tRNA Database Washington (USA)
- Helicobacter PyloriGene World-Wide Web Server Pasteur (French)
- Helicobacter pylori Database of Protein Interactomes (hp-DPI) Taipei (Taiwan)
- Helicobacter pylori 26695 GIB (Japan)
- Summary of Helicobacter pylori, Strain 26695 Maryland (USA)
- Lactobacillus plantarum Nijmegen (The Netherlands)
- LEGER (knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species) Braunschweig (Germany)
- Leptospira (Strain list and Genetic and Physical maps) Pasteur
- ListiList (Listeria Web server) Pasteur
- Methanobacterium thermoautotrophicum Database Ohio (USA)
- Index of Methanococcus jannaschii entries Expasy
- Methanococcus jannaschii Genome Database TIGR
- Methanococcus jannaschii : PEDANT MIPS (Germany)
- Mycobacterium Sanger
- Mycobacterium leprae World-Wide Web Server Pasteur (French)
- Mycobacterium tuberculosis H37Rv Pasteur (French)
- Mycobacterium tuberculosis diversity knowledgebase AmpliBASE MT
- Mycobacterium tuberculosis secreted proteins PHRI (USA)
- MtbRegList (database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis) Sherbrooke (Canada)
- MolliGen (database dedicated to the comparative genomics of Mollicutes) Bordeaux (France)
- Mycoplasma genitalium Genome Database TIGR (USA)
- Myxococcus xanthus Chicago (USA)
- Neisseria gonorrhoeae Oklahoma (USA)
- Neisseria meningitidis Sanger (UK)
- Nitrosomonas europaea JGI-DOE (USA)
- PFGD (functional genomics of phytophthora-plant interactions) Ohio (USA)
- Prochlorococcus marinus JGI-DOE (USA)
- SYSTOMONAS (an integrated database for systems biology analysis of Pseudomonas) Braunschweig (Germany)
- Pseudomonas aeruginosa PGC (USA)
- Pseudomonas fluorescens JGI-DOE (USA)
- PseuRECA (reannotation and context analysis of the Pseudomonas aeruginosa PA01 genome) EBI (UK)
- Pyrococcus abyssi Genoscope (French), see also U-Paris Sud
- Pyrococcus horikoshii OT3 database NITE (Japan)
- Rhizobium : Protein sequence entries in SwissProt Expasy
- Rhizobium meliloti (Sinorhizobium meliloti) INRA (French)
- Rhodobacter sphaeroides Texas (USA)
- Rhodopseudomonas palustris JGI-DOE (USA)
- Rickettsia genome database IGS (French)
- Rickettsia prowazekii GIB (Japan), see also TIGR, see also Protein sequence entries in SwissProt Expasy
- Salmonella enterica serovar Typhimurium Washington (USA)
- Salmonella typhi Sanger (UK)
- Salmonella typhimurium LT2 chromosomal entries and their corresponding StyGene cross-references Expasy
- ShiBASE (an integrated database for comparative genomics of Shigella ) Beijing (China)
- SIDDBASE (database containing the stress-induced DNA duplex destabilization (SIDD) profiles of complete microbial genomes) California (USA)
- Sinorhizobium meliloti INRA-Toulouse (French)
- Staphylococcus aureus NITE (Japan)
- Staphylococcus haemolyticus JCSC1435 NITE (Japan)
- Streptomyces avermitilis MA-4680 NITE (Japan)
- Streptococcus pyogenes Oklahoma (USA)
- Streptomyces coelicolor (ScoDB) JIC (UK)
- Streptomyces avermitilis Kitasato (Japan)
- Sulfolobus database Copenhagen (Denmark)
- Sulfolobus solfataricus : PEDANT MIPS (Germany)
- Sulfolobus solfataricus P2 complete genome sequencing project Paris (French)
- Sulfolobus tokodaii NITE (Japan)
- Synechocystis MIPS (Germany), see also GIB (Japan), see also Index of Synechocystis strain PCC 6803 entries Expasy
- Thermoplasma acidophilum Max-Planck (Germany)
- Thermotoga maritima GD TIGR (USA)
- Tropheryma whipplei Sanger (UK)
- VMD (a community annotation database for oomycetes and microbial genomes) Virginia (USA)
- xBASE (a collection of online databases for bacterial comparative genomics) Birmingham (UK)
- Xylella fastidiosa Genome Project Sao Paulo (Brasil)
- Yersinia pestis Sanger (UK)
- Pufferfish
- Sea lamprey
- Silkworm
- SilkDB (knowledgebase for silkworm biology and genomics) Beijing (China)
- SilkSatDb (microsatellite database of the silkworm, Bombyx mori) Hyderabad (India)
- Viruses
- Emiliania huxleyi virus 86 (EhV86) Southampton (UK)
- Emiliania huxleyi virus 86 (EhV86) Sanger (UK)
- Flavitrack (an annotated database of flavivirus sequences) Texas (USA)
- Genotyping resource for viral sequences NCBI (USA)
- GIB-V (database for comparative analysis of virus genomes) Tokyo (Japan)
- Hepatitis C virus database (HCV) LANL (USA)
- HepSEQ (international public health repository for Hepatitis B) London (UK)
- EuHCVdb (the European hepatitis C virus database) IBCP (French)
- HerpesVirus Database UDEL (USA)
- HERV (Human endogenous retroviruses database) IMG (Czech Republic)
- Anti-HIV compounds Database NIAID (USA)
- HIV Database (Los Alamos) www (AB, CTL, Epitopes and Molecular Immunology)
- HIV Drug Resistance Database LANL (USA)
- HIV (positive selection mutation database) California (USA)
- HIV1 - Human protein interaction database NIAID (USA)
- jpHMM at GOBICS (to detect genomic recombinations in HIV-1) Gottingen (Germany)
- HIV Molecular Immunology LANL (USA)
- HIV Protease Database NIST (USA)
- HIV RT and Protease Sequence Database Stanford (USA)
- HIV Sequence Database LANL (USA)
- HPV Database (Los Alamos) www
- ICTVdB (A Universal Virus Database) NCBI (USA)
- IMV (Wisconsin) www (Classification, Sequences, Alignments, and Phylogenetic Trees of Geminiviridae, Picornaviridae, Potyviridae and Plant Viruses)
- Picornavirus (Seq., 3D struct., Align., Pfam) IAH (England)
- Plant Virus on line Idaho (USA)
- Poxviridae family Alabama (USA)
- Retroviruses ressources NCBI (USA)
- SARS (Severe Acute Respiratory Syndrome) NCBI (USA)
- SV40 T antigen Mutant Pittsburg (USA)
- Tobamoviruses Oklahoma (USA)
- Viperdb (a relational database for structural virology) MMTSB (USA)
- Viral genomes NCBI (USA)
- Viral bioinformatics ressources (databases, tools ..) Victoria (Canada)
- VirGen (comprehensive viral genome resource) Pune (India)
- VirOligo database Oklahoma (USA)
- Virus pages (Asfarviridae, Astroviridae, Caliciviridae, Dicistroviridae, Iflavirus, Morbillivirus, Picornaviridae, Reoviridae, Rhabdoviridae, Sequiviridae) IAH (England)
- ViTa (prediction of host microRNAs targets on viruses) Hsin-Chu (Taiwan)
- Viroids
- Subviral RNA Database Ottawa (Canada)
- Yeast
- Ashbya Genome Database (AGD) : a tool for the yeast community and genome biologists Basel (Switzerland)
- ExpressDB (yeast RNA expression data) Harvard (USA)
- GeneQuiz: automated analysis of Yeast genome EBI (UK)
- Génolevures project Bordeaux (French)
- Links to Yeast WWW sites and to SWISS-PROT entries Expasy
- MPact (the MIPS protein interaction resource on yeast) Neuherberg (Germany)
- MYBS (a comprehensive web server for mining transcription factor binding sites in Yeast) Taipei (Taiwan)
- PROPHECY (database for high-resolution phenomics) Goreborg (Sweden)
- Protein-Protein Interaction YPC (USA)
- Sage (Serial Analysis of Gene Expression) SGD (USA), see also Bielefeld (Germany)
- The Sanger Centre
- SCEPTRANS (an online tool for analyzing periodic transcription in yeast) Dallas (USA)
- TRIPLES (database of TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces) Yale (USA)
- Webminer (database of databases used to study gene expression patterns) Stanford (USA)
- Yeast SGB (Stanford), analysis tools, Snapshot
- Yeast Resource Center Public Data Respository Seattle (USA)
- Yeast Chromosome I SwissProt entries Expasy
- Yeast Chromosome II SwissProt entries Expasy
- Yeast Chromosome III SwissProt entries Expasy
- Yeast Chromosome V SwissProt entries Expasy
- Yeast Chromosome VI SwissProt entries Expasy
- Yeast Chromosome VII SwissProt entries Expasy
- Yeast Chromosome VIII SwissProt entries Expasy
- Yeast Chromosome IX SwissProt entries Expasy
- Yeast Chromosome X SwissProt entries Expasy
- Yeast Chromosome XI SwissProt entries Expasy
- Yeast Chromosome XIII SwissProt entries Expasy
- Yeast Chromosome XIV SwissProt entries Expasy
- Yeast comparative genomics MIT (USA)
- Yeast Genome Project (Complete genome) MIPS (Germany), see also Genome Viewer
- Yeast Gene Duplications Dublin (Ireland)
- Yeast Gene Order Browser Dublin (Ireland)
- Yeast GFP fusion localization database UCSF (USA)
- Yeast Introns UCSC (USA)
- Yeast Membrane Protein Library CBS (USA)
- Yeast protein function assignment UCLA-DOE (USA)
- Yeast Protein Interaction Map Project Washington, see also YRC (USA)
- YEASTRACT (search for transcriptional regulators and consensus tracking) Lisbon (Portugal)
- YGOB (tool for visualising the syntenic context of any gene from seven yeast genomes) Dublin (Ireland)
- yMGV (yeast microarray global viewer) ENS (French)
- YPL (Yeast Protein Localization database) Graz (Austria)
- YTPdb (Yeast Transport Protein db) ULB (Belgium)
- Worm-Yeast Protein Comparison Stanford (USA)
- SRS (linked libraries : YeastCDNA - Yeast_Ensembl_CDNA - Yeast_Ensembl_Prot - Yeast_ORF_Layout) DKFZ (Germany)
- Candida albicans
- Candida albicans IRB (Canada)
- CandidaDB (genome database for Candida albicans pathogenomics) Pasteur (French)
- Candida albicans genome annotation California (USA)
- Candida Genome Database (CGD) Stanford (USA)
- Candida albicans physical map Minnesota (USA)
- Links to C.albicans WWW sites and to SWISS-PROT entries Expasy
- Sequencing of Candida Albicans Stanford (USA)
- Saccharomyces
- EUROSCARF Frankfurt (Germany)
- GeneCensus (compilation of ORF data) Yale (USA)
- PEDANT MIPS (Germany)
- SCMD (Morphological Database) Tokyo (Japan)
- SCPD (Promoter Database of Saccharomyces cerevisiae) CSHL (USA)
- SGD Stanford (USA)
- Small Nucleolar RNAs (snoRNAs) Massachusetts (USA)
- Schizosaccharomyces pombe
- Forsburg Lab pombe pages California (USA)
- SwissProt entries Expasy
- Schizosaccharomyces pombe GeneDB Sanger (UK)
- S. pombe Genome Project Sanger (UK)
- Tetraodon
- Xenopus
- Axeldb (Xenopus laevis) DKFZ (Germany)
- Trans-NIH Xenopus initiative NIH (USA)
- Xenopus tropicalis Ensembl
- Xenopus web resource xenbase
- Zebrafish
- Ensembl
- GeneNest Index (EST Clustering Projects) Max-Planck (Germany)
- Vega Zebrafish Sanger (UK)
- Wanda (database of duplicated genes in fish) Konstaz (Germany)
- WashU-Zebrafish Genome Resources Project Washington (USA)
- ZI (Harvard) www (USA)
- The Zebrafish Information Network zfin
- Zebrafish Microsatellite Maps Harvard (USA)
- Zebrafish Project Stanford (USA)
- Comparative Genome Databases
- COMPARE (a multi-organism system for cross-species data comparison and transfer of information) IBDML (French)
- Comparative Genomics (dbERGE, Enterix, Etope, Gala, HbVar, Mulan, RPscores) Pennsylvania (USA)
- EGO (eukaryotic gene orthologs) TIGR (USA)
- Gene-map Homology Search NIAI (Japan)
- HOINVGEN (database of homologous invertebrate genes) PBIL (France)
- HomoloGene (orthologs and homologs for genes represented in UniGene and LocusLink for human, mouse, rat, and zebrafish) NCBI (USA)
- Human and Nematode Orthologs NCBI (USA)
- InParanoid (Database of pairwise orthologs) CGR (Sweden)
- OMA (Browser-Exploring orthologous relations across 352 complete genomes) ETHZ (Switzerland)
- TAED (Adaptive Evolution Database) Bergen (Norway)
- XLocus (an interspecies cross-reference of similar loci) (Yale)
- ZooDDD (a cross-species database for digital differential display analysis) Taipei (Taiwan)
- Microarrays
- ArrayExpress (public repository for microarray data) EBI (UK)
- ChipDB - Gene expression db MIT (USA)
- Dragon database (Database Referencing of Array Genes ON line) KKI (USA)
- ExpressDB - Yeast and E.coli RNA expression db Harvard (USA)
- GeneAnnot (comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes) Weizmann (Israel)
- GEO - Gene Expression Omnibus NCBI (USA)
- GermOnline (database that provides access to microarray expression data from experiments relevant for the mitotic and meiotic cell cycle as well as gametogenesis), Tokyo (Japan) mirror at Stanford (USA)
- ITTACA (database for integrated tumor transcriptome array and clinical data analysis) Institut Curie (French)
- Microarray facility Sanger (UK)
- MUSC DNA Microarray Database Carolina (USA)
- PEPR (GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface) Washington (USA)
- ProbeMatchDB (database for finding equivalent probes across microarray platforms and species) Michigan (USA)
- RAD - RNA abundance db CBIL (USA)
- SMD - Stanford microarray db Stanford (USA)
- TELiS database (expression-based monitoring of transcription factor activity) UCLA (USA)
- Xenopus Microarray Project Rockefeller (USA)
Other
- Aberrant Splicing Database of mammalian genes IMCB (Japan)
- ACLAME (collection and classification of mobile genetic elements (MGEs)) Brussels (Belgium)
- ACeDB Databases INRA, see also Heidelberg, see also Sanger
- AgBase (a unified resource for functional analysis in agriculture) Mississippi (USA)
- ALPSbase : Database of mutations causing human ALPS NHGRI-NIH (USA)
- Alternate Transcript Diversity (Human, Mouse) EBI (UK)
- Alternative splicing DB LBL (USA)
- AMiGA (the arthropodan mitochondrial genomes accessible database) Sao Paulo (Brazil)
- Annotated Genomes ORNL (USA)
- ARGONAUTE (a database for gene regulation by mammalian micro-RNAs) Heidelberg (Germany)
- ArrayExpress Database EBI (UK)
- ASAP II (analysis and comparative genomics of alternative splicing in 15 animal species) California (USA)
- ASTRA (Alternative Splicing and TRanscription Archives - Human, mouse, Drosophila, C. elegans, Arabidopsis, O. sativa) Tokyo (Japan)
- Bacteria: Systematics Berkeley (USA)
- Bioverse (exploring the relationships among the molecular and genomic, proteomic, systems, and organismal worlds) Washington (USA)
- BodyMap-Xs (anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression) Shizuoka (Japon)
- BRITE (Biomolecular Relations in Information Transmission and Expression) GenomeNet (Japan)
- BROP (oral pathogens) Boston (USA)
- The Cancer Genome Anatomy Project (CGAP) NCBI (USA)
- CBS Databases (Filamentous fungi, Yeast, Bacteria, Aphyllophorales, Fusarium, Phabagen Collection) CBS (The Netherlands)
- Clone Registry (Homo sapiens, Mus musculus, Rattus norvegicus) NCBI (USA)
- Comparative Genometrics Lausane (Switzerland)
- Comparative Genomics (dbERGE, Enterix, Etope, Gala, HbVar, Mulan, RPscores) Pennsylvania (USA)
- Complete Mitochondrial Sequences at NCBI
- CORG (COmparative Regulatory Genomics : multi-species DNA comparison and annotation) Max Planck Institute (Germany)
- DEG (database of essential genes) Tianjin (China)
- dbERGE II (Database of Experimental Results for Gene Expression) Pennsylvania (USA)
- DOGS (Database Of Genome Sizes) CBS (Denmark)
- DBTSS (dataBase of transcriptional start sites) Tokyo (Japan)
- DBD (a transcription factor prediction database) Cambridge (UK)
- DED (Database of Evolutionary Distances) Pennsylvania (USA)
- ECRbase (database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes) Livermore (USA)
- EGO (eukaryotic gene orthologs) TIGR (USA)
- Entrez genome NCBI (USA), see also HomoloGene
- Entrez genome project NCBI
- Environmental Genome Project (EGP) NIEHS (USA)
- ERGDB (Estrogen Responsive Genes Database) KELIIR (Singapore)
- eSLDB (eukaryotic subcellular localization database) Bologna (Italy)
- Pathology Cytogenetics Resources UW (USA)
- GeneDB (resources for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei) WTFGDI
- GeneX (gene expression database) NCGR (USA)
- GEO (Gene Expression Omnibus) NCBI (USA)
- Gene ontology EBI-EMBL
- Genome Atlas Database CBS (Denmark)
- The Genome Channel ORNL (USA)
- Genome Information Broker (more 338 species) GIB (Japan)
- Genome Projects Sanger (UK)
- Genomic Database Search (Pig, Cattle, Horse, Mouse, Human) www (Japan)
- Genome Reviews (provides up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes) EBI (UK)
- The Genomic Threading Database (contains structural annotations of proteomes, translated from the genomes of key organisms) London (UK)
- Genomic tRNA Database (GtRDB) UCSC (USA)
- GenLine (Electronic clinical genetics knowledge base) Washington (USA)
- GOBASE (a database of organelle and bacterial genome information) Montréal (Canada)
- GOLD (Genomes On Line Database) Illinois (USA)
- GOToolBox (functional Investigation of Gene Datasets) LGPD (French)
- GRSDB (a database of quadruplex forming G-rich sequences in alternatively processed mammalian pre-mRNA sequences) New Jersey (USA)
- GTOP (Genomes TO Protein structures and functions) NIG (Japan)
- Homeodomain Resource NHGRI (USA)
- HvrBase++ (a phylogenetic database for primate species) Vienna (Austria)
- Immigrant: The database of immigrant genes Bioinformatics
- IGMS (Integrated Genetic Map Service) Berlin (Germany)
- Integrated Taxonomic Information System (ITIS) USDA (USA)
- iTOL (interactive Tree Of Life : an online tool for phylogenetic tree display and annotation) EMBL (Germany)
- KEGG (Kyoto Encyclopedia of Genes and Genomes) GenomeNet (Japan)
- LIFEdb (Localization, Interaction, Functional assays and Expression of Proteins) Heidelberg (Germany)
- Magpie (Automated Genomics Project Investigation Environment) Calgary (Canada)
- Mammalian Gene Mutation Database (MGMD) Swansea (UK)
- Mammalian Orthology and Comparative Maps MGI (USA)
- MamMiBase (a mitochondrial genome database for mammalian phylogenetic studies) Rio de Janeiro (Brasil)
- MAPPER (putative transcription factor binding sites in multiple genomes) Boston (USA)
- Megx.net (database resources for marine ecological genomics) Bremen (Germany)
- MethDB (DNA Methylation Database) Montpellier (French)
- miRGen (a database for the study of animal microRNA genomic organization and function) Pennsylvania (USA)
- MitoP2 (the mitochondrial proteome database - yeast, mouse, human) Munich (Germany)
- MPPI (Mammalian Protein-Protein Interaction Database) MIPS (Germany)
- MLST (Multi Locus Sequence Typing : unambiguous characterisation of isolates of bacteria and other organisms) London (UK)
- MPromDb (an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data) Ohio (USA)
- NATsDB (Natural Antisense Transcripts DataBase) Beijing (China)
- ncRNA (RNAdb : a comprehensive mammalian noncoding RNA database) Queensland (Australia)
- NMPDR (National Microbial Pathogen Data Resource) NCSA (USA)
- NONCODE (an integrated knowledge database of non-coding RNAs) Beijing (China)
- ODB (database of operons accumulating known operons across multiple genomes) Kyoto (Japan)
- Organelle DB (a cross-species database of protein localization and function) Michigan (USA)
- OGRe (Organellar Genome Retrieval system) McMaster (Canada)
- OMGProm (a database of orthologous mammalian gene promoters) Ohio (USA)
- OMIA (Online Mendelian Inheritance in Animals) ANGIS (Australia)
- OmicBrowse (a browser of multidimensional omics annotations) RIKEN (Japon)
- Omic space (coordinate-based integration and analysis of genomic phenomic interactions : H. sapiens, M. musculus, C. elegans, A. thalania) RIKEN (Japan)
- OriDB (a DNA replication origin database) Aberdeen (Scotland)
- Orthologous Promoters, DoOP (collections of clusters of orthologous upstream sequences from chordates and plants) Budapest (Hungary)
- OrthoMCL-DB (querying a comprehensive multi-species collection of ortholog groups) Pennsylvania (USA)
- PA-GOSUB (database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization) Alberta (Canada)
- PAIdb (pathogenicity islands) Daejeon (Korea)
- PartiGeneDB (collating partial genomes) Toronto (Canada)
- PATRIC (the VBI pathosystems resource integration center) Virginia (USA)
- PeroxisomeDB (a database for the peroxisomal proteome, functional genomics and disease) Barcelona (Spain)
- Pfam : taxonomy query Sanger (UK)
- PhenomicDB (a new cross-species genotype/phenotype resource) Berlin (Germany)
- PHI-base (a database for pathogen host interactions) Harpenden (UK)
- PolyA_DB (a database for mammalian mRNA polyadenylation) New Jersey (USA)
- Polymorphix (a sequence polymorphism database) PBIL (French)
- PopSet (analyse the evolutionary relatedness of a population NCBI (USA)
- PReMod (a database of genome-wide mammalian cis-regulatory module predictions) Montréal (Canada)
- ProtEST (protein matches for ESTs : Human, rat, mouse, zebrafish, cow, frog, cress, rice, wheat, barley, maize) NCBI (USA)
- pSTIING (a systems approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer) London (UK)
- PUMA2 (grid-based high-throughput analysis of genomes and metabolic pathways) Argonne (USA)
- Reactome (a knowledgebase of biological processes) CSHL-EBI-GOC (USA)
- Recode (database of the translational recoding events) Utah (USA)
- RefDIC (open-access database that integrates cross-reference information from the transcriptome and proteome of immune cells) RIKEN (Japan)
- RNAdb 2.0 (an expanded database of mammalian non-coding RNAs) Queensland (Australia)
- rSNP Guide (Transcription Factor Binding to DNA with Variations) ICG (Russian)
- SAGE (Serial Analysis of Gene Expression) NCBI, see also Sagenet
- Sebida (database for the functional and evolutionary analysis of genes with sex-biased expression) Martinsried (Germany)
- SEED (an annotation/analysis tool) Chicago (USA)
- Sentra (database of signal transduction proteins for comparative genome analysis) Argonne (USA)
- SGDB (a database of synthetic genes re-designed for optimizing protein over-expression) Maryland (USA)
- Shigen databases (Vector, animals, fish, drosphila, plants, ...) Mishima (Japan)
- siRecords (an extensive database of mammalian siRNAs with efficacy ratings) Minnesota (USA)
- siRNAdb (a database of siRNA sequences) Stockholm (Sweden)
- Sno/scaRNAbase (a curated database for small nucleolar RNAs and cajal body-specific RNAs) Shanghai (China)
- SNPSTR (a database of compound microsatellite-SNP markers : human, dog, mouse, rat and chicken) London (UK)
- SPEED (a molecular-evolution-based database of mammalian orthologous groups) Kansas (USA)
- STD (huamn sexually transmitted bacteria and viruses) LANL (USA)
- SwissRegulon (a database of genome-wide annotations of regulatory sites) Basel (Switzerland)
- Taxonomy Database NCBI (GenBank)
- Taxonomy Workbench IMP (Austria)
- TBestDB (a taxonomically broad database of expressed sequence tags (ESTs)) Montreal (Canada)
- Telomere Database Genlink (USA)
- TGD : Tumor Gene Database BCM, another link (database of genes associated with tumorigenesis and cellular transformation)
- TIGR Database (Institute for Genomic Research) databases (links between source, collection, taxonomy, and molecular sequence data), see also CMR genomes
- TIGR Gene Indices (clustering and assembling EST and known genes and integration with eukaryotic genomes) TIGR
- TimeTree (a knowledge-base of divergence times among organisms) Pennsylvania (USA)
- TMBETA-GENOME (database for annotated beta-barrel membrane proteins in genomic sequences) Tokyo (Japan)
- Transgenic and Targeted Mutant Animal Database ORNL (Oak Ridge)
- TRED (a Transcriptional Regulatory Element Database and a platform for in silico gene regulation studies) CSHL (USA)
- TreeBase (relational database of phylogenetic information) Buffalo (USA)
- TreeFam (a curated database of phylogenetic trees of animal gene families) Sanger (UK)
- Tree of life tolweb
- U12DB (a database of orthologous U12-type spliceosomal introns) Barcelona (Spain)
- UniGene (system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters) NCBI (USA)
- Viral Diseases of Insects in the Literature (VIDIL) Illinois (USA)
- The Visible Human Project NCBI (USA)
- XPRO (database of eukaryotic protein-encoding DNA sequences in GenBank) NUS (Singapore)
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