| Major sequence repositories |
|
|
| DNA Data Bank of Japan (DDBJ) |
http://www.ddbj.nig.ac.jp |
All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration |
| EMBL Nucleotide Sequence Database |
http://www.ebi.ac.uk/embl.html |
All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration |
| GenBank |
http://www.ncbi.nlm.nih.gov/ |
All known nucleotide and protein sequences; International Nucleotide Sequence Database Collaboration |
| NCBI Reference Sequence Project |
http://www.ncbi.nlm.nih.gov/RefSeq/ |
Non-redundant collection of naturally-occurring biological molecules |
| Ensembl |
http://www.ensembl.org/ |
Annotated information on eukaryotic genomes |
| UCSC Genome Browser |
http://genome.ucsc.edu/ |
Genome assemblies and annotation |
| STACK |
http://www.sanbi.ac.za/Dbases.html |
Non-redundant, gene-oriented clusters |
| TIGR Gene Indices |
http://www.tigr.org/tdb/tgi.shtml |
Non-redundant, gene-oriented clusters |
| UniGene |
http://www.ncbi.nlm.nih.gov/UniGene/ |
Non-redundant, gene-oriented clusters |
| Comparative Genomics |
|
|
| Clusters of Orthologous Groups (COG) |
http://www.ncbi.nlm.nih.gov/COG |
Phylogenetic classification of proteins from 43 complete genomes |
| CORG |
http://corg.molgen.mpg.de |
Conserved non-coding sequence blocks |
| Homophila |
http://homophila.sdsc.edu |
Relationship of human disease genes to genes in Drosophila |
| MBGD |
http://mbgd.genome.ad.jp |
Microbial genome database for comparative genomic analysis |
| ParaDB |
http://abi.marseille.inserm.fr/paradb/ |
Paralogy mapping in human genomes |
| XREFdb |
http://www.ncbi.nlm.nih.gov/XREFdb/ |
Cross-referencing of model organism genetics with mammalian phenotypes |
| Gene Expression |
|
|
| ArrayExpress |
http://www.ebi.ac.uk/arrayexpress |
Public collection of microarray gene expression data |
| Axeldb |
http://www.dkfz-heidelberg.de/abt0135/axeldb.htm |
Gene expression in Xenopus |
| BodyMap |
http://bodymap.ims.u-tokyo.ac.jp/ |
Human and mouse gene expression data |
| EPConDB |
http://www.cbil.upenn.edu/EPConDB |
Endocrine pancreas consortium database |
| FlyView |
http://pbio07.uni-muenster.de/ |
Drosophila development and genetics |
| Gene Expression Database (GXD) |
http://www.informatics.jax.org/menus/expression_menu.shtml |
Mouse gene expression and genomics |
| HugeIndex |
http://hugeindex.org |
mRNA expression levels of human genes in normal tissues |
| Interferon Stimulated Gene Database |
http://www.lerner.ccf.org/labs/williams/xchip-html.cgi |
Genes induced by treatment with interferons |
| Kidney Development Database |
http://golgi.ana.ed.ac.uk/kidhome.html |
Kidney development and gene expression |
| MAGEST |
http://www.genome.ad.jp/magest |
Ascidian (Halocynthia roretzi) gene expression patterns |
| MEPD |
http://medaka.dsp.jst.go.jp/MEPD |
Gene expression data from the small freshwater fish Medaka (Oryzias latipes) |
| MethDB |
http://www.methdb.de |
DNA methylation data, patterns and profiles |
| Mouse Atlas and Gene Expression Database |
http://genex.hgu.mrc.ac.uk |
Spatially-mapped gene expression data |
| MTID |
http://mouse.ccgb.umn.edu/transposon/ |
Sleeping beauty transposon insertions in mice |
| NetAffx |
http://www.affymetrix.com |
Public Affymetrix probesets and annotations |
| RECODE expression |
http://recode.genetics.utah.edu |
Genes using programmed translational recoding in their expression |
| SeedGenes |
http://www.seedgenes.org |
Genes essential for Arabidopsis development |
| Stanford Microarray Database |
http://genome-www.stanford.edu/microarray |
Raw and normalized data from microarray experiments |
| Tooth Development Database |
http://bite-it.helsinki.fi/ |
Gene expression in dental tissue |
| TRANSPATH |
http://www.biobase.de/pages/products/databases.html |
Gene regulatory networks and microarray analysis |
| TRIPLES |
http://ygac.med.yale.edu |
TRansposon-insertion phenotypes, localization, and expression in Saccharomyces |
| Gene Identification and Structure |
|
|
| AllGenes |
http://www.allgenes.org |
Human and mouse gene index integrating gene, transcript and protein annotation |
| Ares Lab Yeast Intron Database |
http://www.cse.ucsc.edu/research/compbio/yeast_introns.htmlyeast_introns.html |
Splicesomal introns in Saccharomyces cerevisiae |
| ASAP |
http://www.bioinformatics.ucla.edu/ASAP |
Alternative spliced isoforms |
| CUTG |
http://www.kazusa.or.jp/codon/ |
Codon usage tables |
| DBTBS |
http://elmo.ims.u-tokyo.ac.jp/dbtbs/ |
Bacillus subtilis binding factors and promoters |
| EID |
http://mcb.harvard.edu/gilbert/EID/ |
Protein-coding, intron-containing genes |
| EPD |
http://www.epd.isb-sib.ch/ |
Eukaryotic POL II promoters with experimentally-determined transcription start sites |
| ExInt |
http://intron.bic.nus.edu.sg/exint/exint.html |
Exon–intron structure of eukaryotic genes |
| Gene Resource Locator |
http://grl.gi.k.u-tokyo.ac.jp |
Alignment of ESTs with finished human sequence |
| HS3D |
http://www.sci.unisannio.it/docenti/rampone/ |
Human exon, intron and splice regions |
| HUNT |
http://www.hri.co.jp/HUNT |
Annotated human full-length cDNA sequences |
| HvrBase |
http://www.hvrbase.org |
Primate mtDNA control region sequences |
| IDB/IEDB |
http://nutmeg.bio.indiana.edu/intron/index.html |
Intron sequence and evolution |
| MICdb |
http://www.cdfd.org.in/micas |
Prokaryotic microsatellites |
| PACRAT |
http://www.biosci.ohio-tate.edu/~pacrat |
Archaeal and bacterial intergenic sequence features |
| PLACE |
http://www.dna.affrc.go.jp/htdocs/PLACE |
Plant cis-acting regulatory elements |
| PlantCARE |
http://oberon.rug.ac.be:8080/PlantCARE/ |
Plant cis-acting regulatory elements |
| PlantProm |
http://mendel.cs.rhul.ac.uk/ |
Proximal promoter sequences for RNA polymerase II |
| PromEC |
http://bioinfo.md.huji.ac.il/marg/promec |
Escherichia coli mRNA promoters with experimentally-identified transcriptional start sites |
| RRNDB |
http://rrndb.cme.msu.edu |
Variation in prokaryotic ribosomal RNA operons |
| rSNP Guide |
http://util.bionet.nsc.ru/databases/rsnp.html |
Single nucleotide polymorphisms in regulatory gene regions |
| RTPrimerDB |
http://www.realtimeprimerdatabase.ht.st/ |
Validated PCR primer and probe sequence records |
| SNP Consortium database |
http://snp.cshl.org |
SNP Consortium data |
| SpliceDB |
http://genomic.sanger.ac.uk/spldb/SpliceDB.html |
Canonical and non-canonical mammalian splice sites |
| Sputnik |
http://mips.gsf.de/proj/sputnik |
Functional annotation of clustered plant ESTs |
| STRBase |
http://www.cstl.nist.gov/div831/strbase/ |
Short tandem DNA repeats |
| TRANSCompel |
http://www.gene-regulation.com/pub/databases.html#transcompel |
Composite regulatory elements |
| Transterm |
http://uther.otago.ac.nz/Transterm.html |
Codon usage, start and stop signals |
| TRRD |
http://www.bionet.nsc.ru/trrd/ |
Transcription regulatory regions of eukaryotic genes |
| VIDA |
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html |
Virus genome open reading frames |
| WormBase |
http://www.wormbase.org |
Guide to Caenorhabditis elegans biology |
| YIDB |
http://www.EMBL-Heidelberg.DE/ExternalInfo/seraphin/yidb.html |
Yeast nuclear and mitochondrial intron sequences |
| Genetic and Physical Maps |
|
|
| DRESH |
http://www.tigem.it/LOCAL/drosophila/dros.html |
Human cDNA clones homologous to Drosophila mutant genes |
| G3-RH |
http://www-shgc.stanford.edu/RH/ |
Stanford G3 and TNG radiation hybrid maps |
| GB4-RH |
http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml |
Genebridge4 (GB4) human radiation hybrid maps |
| GDB |
http://www.gdb.org |
Human genes and genomic maps |
| GenAtlas |
http://www.citi2.fr/GENATLAS/ |
Human genes, markers and phenotypes |
| GeneMap '99 |
http://www.ncbi.nlm.nih.gov/genemap/ |
International Radiation Mapping Consortium human gene map |
| Genetpig |
http://www.infobiogen.fr/services/Genetpig |
Comparative mapping in pig (Sus scrofa) |
| GenMapDB |
http://genomics.med.upenn.edu/genmapdb |
Mapped human BAC clones |
| HuGeMap |
http://www.infobiogen.fr/services/Hugemap |
Human genome genetic and physical map data |
| IXDB |
http://ixdb.mpimg-berlin-dahlem.mpg.de |
Physical maps of human chromosome X |
| RHdb |
http://www.ebi.ac.uk/RHdb |
Radiation hybrid map data |
| The Unified Database (UDB) |
http://bioinfo.weizmann.ac.il/udb/ |
Integrated human maps |
| Genomic Databases |
|
|
| ACeDB information |
http://www.acedb.org/ |
Caenorhabditis elegans, Schizosaccharomyces pombe, and human sequences and genomic information |
| AMmtDB |
http://bighost.area.ba.cnr.it/mitochondriome |
Metazoan mitochondrial genes |
| ArkDB |
http://www.thearkdb.org/ |
Genome databases for farm and other animals |
| ASAP |
https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm |
Systematic annotation package for community-based annotation and analysis of genomes |
| BSD |
http://bsd.cme.msu.edu |
Comparative data on known biodegradative organisms |
| CATMA |
http://www.catma.org |
Arabidopsis gene sequence tags (GSTs) |
| CnidBase |
http://www.cnidome.bu.edu/ |
Cnidarian evolutionary genomics and gene expression |
| Comprehensive Microbial Resource |
http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl |
Completed microbial genomes |
| CropNet |
http://ukcrop.net/ |
Genome mapping in crop plants |
| CroW 21 |
http://bioinfo.weizmann.ac.il/crow21/ |
Human chromosome 21 database |
| CyanoBase |
http://www.kazusa.or.jp/cyano/ |
Synechocystis sp. genome |
| EcoGene |
http://bmb.med.miami.edu/EcoGene/EcoWeb/ |
E. coli K-12 sequences |
| EMGlib |
http://pbil.univ-lyon1.fr/emglib/emglib.html |
Completely-sequenced prokaryotic genomes |
| ERGO |
http://ergo.integratedgenomics.com/ERGO |
Integrated biological data from genomic, biochemical, expression, and genetic experiments, and from the literature |
| FlyBase |
http://flybase.bio.indiana.edu/ |
Drosophilaysequences andgenomic information |
| Full-Malaria |
http://fullmal.ims.u-tokyo.ac.jp |
Full-length cDNA library from erythrocytic-stage Plasmodium falciparum |
| GeneCards |
http://bioinfo.weizmann.ac.il/cards/ |
Integrated database of human genes, maps, proteins and diseases |
| Genew |
http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl |
Approved symbols for all human genes |
| GOBASE |
http://megasun.bch.umontreal.ca/gobase/gobase.html |
Organelle genome database |
| GOLD |
http://igweb.integratedgenomics.com/GOLD/ |
Information regarding complete and ongoing genome projects |
| GénoPlante-Info |
http://genoplante-info.infobiogen.fr |
Plant genomic data derived from the Génoplante consortium |
| GrainGenes |
http://www.graingenes.org |
Genomic database for small-grain crops |
| HGT-DB |
http://www.fut.es/~debb/HGT/ |
Putative horizontally-transferred genes in prokaryotic genomes |
| HIV Sequence Database |
http://hiv-web.lanl.gov/ |
HIV RNA sequences |
| HOWDY |
http://www-alis.tokyo.jst.go.jp/HOWDY/ |
Integrated human genomic information |
| Human BAC Ends Database |
http://www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html |
Non-redundant human BAC end sequences |
| ICB |
http://www.mbio.co.jp/icb |
Prokaryotic protein-coding gene data |
| INE |
http://rgp.dna.affrc.go.jp/giot/INE.html |
Integrated database for rice genome analysis and sequencing |
| IRIS |
http://www.iris.irri.org |
Rice germplasm geneology and field data; rice structural and functional genomics and proteomics |
| Medicago Genome Initiative (MGI) |
http://xgi.ncgr.org/mgi |
Model legume Medicago ESTs, gene expression and proteomic data |
| Mendel Database family |
http://www.mendel.ac.uk/ |
Database of plant EST and STS sequences annotated with gene family information |
| MIPS |
http://www.mips.biochem.mpg.de/ |
Protein and genomic sequences |
| MitBASE |
http://www3.ebi.ac.uk/Research/Mitbase/mitbase.pl |
Mitochondrial genomes, intra-species variants, and mutants |
| MitoDat |
http://www-lecb.ncifcrf.gov/mitoDat/ |
Mitochondrial proteins (predominantly human) |
| MITOMAP |
http://www.gen.emory.edu/mitomap.html |
Human mitochondrial genome |
| MitoNuc/MitoAln |
http://bio-www.ba.cnr.it:8000/BioWWW/#MitoNuc |
Nuclear genes coding for mitochondrial proteins |
| MITOP |
http://www.mips.biochem.mpg.de/proj/medgen/mitop/ |
Mitochondrial proteins, genes and diseases |
| MOsDB |
http://mips.gsf.de/proj/rice |
Oryza sativa genome |
| Mouse Genome Database (MGD) |
http://www.informatics.jax.org |
Mouse genetics, genomics, alleles and phenotypes |
| MtDB |
http://www.medicago.org/MtDB |
Medicago trunculata genome |
| NRSub |
http://pbil.univ-lyon1.fr/nrsub/nrsub.html |
B. subtilis genome |
| OGRe |
http://www.bioinf.man.ac.uk/ogre |
Complete mitochondrial genome sequences for 200 metazoan species |
| Oryzabase |
http://www.shigen.nig.ac.jp/rice/oryzabase/ |
Rice genetics and genomics |
| PEDANT genome database |
http://pedant.gsf.de |
Automated analysis of genomic sequences |
| Phytophthora Genome Consortium Database |
https://xgi.ncgr.org/pgc |
ESTs from Phytophthora infestans and Phytophthora sojae |
| PlantGDB |
http://zmdb.iastate.edu/PlantGDB/ |
Actively-transcribed plant genomic sequences |
| PlasmoDB |
http://PlasmoDB.org |
Plasmodium genome |
| Proteome BioKnowledge Library |
http://www.proteome.com |
Model organism pathogen, and mammalian proteomes |
| Rat Genome Database |
http://rgd.mcw.edu |
Rat genetic and genomic data |
| RiceGAAS |
http://RiceGaas.dna.affrc.go.jp/ |
Rice genome sequence |
| RsGDB |
http://www-mmg.med.uth.tmc.edu/sphaeroides |
Rhodobacter sphaeroides genome |
| RTPrimerDB |
http://www.realtimeprimerdatabase.ht.st |
Real-time PCR primer and probe sequences |
| Saccharomyces Genome Database |
http://genome-www.stanford.edu/Saccharomyces/ |
Saccharomyces cerevisiae genome |
| SOURCE |
http://source.stanford.edu |
Functional genomic resource for annotations ontologies, and expression data |
| SubtiList |
http://genolist.pasteur.fr/SubtiList/ |
Bacillus subtilis 168 genome |
| The Arabidopsis Information Resource (TAIR) |
http://www.arabidopsis.org/ |
Arabidopsis thaliana genome |
| TIGR Microbial Database |
http://www.tigr.org/tdb/mdb/mdbcomplete.html |
Microbial genomes and chromosomes |
| TIGR Rice Genome Annotation Resource |
http://www.tigr.org/tdb/e2k1/osa1/ |
Rice sequence, BAC/PAC clones and related mapping data |
| ToxoDB: The Toxoplasma gondii Genome Database |
http://ToxoDB.org |
Apicomplexan parasite Toxoplasma gondii genome |
| WILMA |
http://www.came.sbg.ac.at/wilma/ |
Caenorhabditis elegans annotation |
| WorfDB |
http://worfdb.dfci.harvard.edu |
Caenorhabditis elegans ORFeome |
| WormBase |
http://www.wormbase.org/ |
Genomic data on C. elegans and related nematodes |
| ZFIN |
http://zfin.org/ |
Genetic, genomic and developmental data from zebrafish |
| ZmDB |
http://zmdb.iastate.edu/ |
Maize genome database |
| Intermolecular Interactions |
|
|
| BIND |
http://bind.ca |
Molecular interactions, complexes and pathways |
| Database of Interacting Proteins (DIP) |
http://dip.doe-mbi.ucla.edu |
Experimentally-determined protein–protein interactions |
| Database of Ribosomal Crosslinks (DRC) |
http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/ |
Ribosomal crosslinking data |
| DPInteract |
http://arep.med.harvard.edu/dpinteract/ |
Binding sites for E. coli DNA-binding proteins |
| InterDom |
http://InterDom.lit.org.sg |
Putative protein domain interactions |
| JenPep |
http://www.jenner.ac.uk/Jenpep2 |
Functional and quantitative thermodynamic data on peptide binding to immunological biomacromolecules |
| KDBI |
http://xin.cz3.nus.edu.sg/group/kdbi.asp |
Kinetic data on biomolecular interactions |
| MHC—Peptide Interaction Database |
http://surya.bic.nus.edu.sg/mpid |
Class I and Class II MHC-peptide complexes |
| STRING |
http://www.bork.embl-heidelberg.de/STRING/ |
Predicted functional associations between proteins |
| Metabolic Pathways and Cellular Regulation |
|
|
| EcoCyc |
http://ecocyc.org/ |
Escherichia coli K-12 genome, metabolic pathways, transporters and gene regulation |
| ENZYME |
http://www.expasy.ch/enzyme/ |
Enzyme nomenclature |
| EpoDB |
http://www.cbil.upenn.edu/EpoDB/ |
Genes expressed during human erythropoiesis |
| Klotho |
http://www.ibc.wustl.edu/klotho/ |
Collection and categorization of biological compounds |
| Kyoto Encyclopedia of Genes and Genomes (KEGG) |
http://www.genome.ad.jp/kegg |
Metabolic and regulatory pathways |
| LIGAND |
http://www.genome.ad.jp/ligand/ |
Chemical compounds and reactions in biological pathways |
| MetaCyc |
http://ecocyc.org/ |
Metabolic pathways and enzymes from various organisms |
| The University of Minnesota Biocatalysis Biodegradation Database |
http://umbbd.ahc.umn.edu/ |
Curated information on microbial catabolismand related biotransformations |
| PathDB |
http://www.ncgr.org/pathdb |
Biochemical pathways, compounds and metabolism |
| PRODORIC |
http://prodoric.tu-bs.de |
Prokaryotic database of gene regulation and regulatory networks |
| RegulonDB |
http://www.cifn.unam.mx/Computational_Genomics/regulondb/ |
Escherichia coli transcriptional regulation and operon organization |
| UM-BBD |
http://umbbd.ahc.umn.edu/ |
Microbial biocatalytic reactions and biodegradation pathways |
| WIT2 |
http://wit.mcs.anl.gov/WIT2/ |
Integrated system for metabolic models |
| Mutation Databases |
|
|
| ALFRED |
http://alfred.med.yale.edu |
Allele frequencies and DNA polymorphisms |
| Androgen Receptor Gene Mutations Database |
http://www.mcgill.ca/androgendb/ |
Mutations in the androgen receptor gene |
| Asthma Gene Database |
http://cooke.gsf.de/asthmagen/main.cfm |
Linkage and mutation studies on the genetics of asthma and allergy |
| Atlas of Genetics and Cytogenetics in Oncology and Haematology |
http://www.infobiogen.fr/services/chromcancer/ |
Chromosomal abnormalities in oncologyand haematology |
| BTKbase |
http://bioinf.uta.fi/BTKbase/ |
Mutation registry for X-linked agammaglobulinemia |
| CASRDB |
http://data.mch.mcgill.ca/casrdb/ |
CASR mutations causing FHH, NSHPT and ADH |
| Database of Germline p53 Mutations |
http://www.lf2.cuni.cz/win/projects/germline_mut_p53.htm |
Mutations in human tumor and cell line p53 gene |
| dbSNP |
http://www.ncbi.nlm.nih.gov/SNP/ |
Single nucleotide polymorphisms |
| FLAGdb/FST |
http://genoplante-info.infobiogen.fr |
Arabidopsis thaliana T-DNA transformants |
| GRAP Mutant Databases |
http://tinyGRAP.uit.no/GRAP/ |
Mutants of family A G-Protein Coupled Receptors (GRAP) |
| Haemophila B Mutation Database IX |
http://www.umds.ac.uk/molgen/haemBdatabase.htm |
Point mutations, short additions and deletions in the Factor IX gene |
| HGVbase |
http://hgvbase.cgb.ki.se |
Curated human polymorphisms |
| HIV-RT |
http://hivdb.stanford.edu/hiv/ |
HIV reverse transcriptase and protease sequence variation |
| Human Gene Mutation Database (HGMD) |
http://www.hgmd.org |
Known (published) gene lesions underlying human inherited disease |
| Human p53/hprt, rodent lacI/lacZ databases |
http://www.ibiblio.org/dnam/mainpage.html |
Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations |
| Human PAX2 Allelic Variant Database |
http://www.hgu.mrc.ac.uk/Softdata/PAX2/ |
Mutations in human PAX2 gene |
| Human PAX6 Allelic Variant Database |
http://www.hgu.mrc.ac.uk/Softdata/PAX6/ |
Mutations in human PAX6 gene |
| Human Type I and III Collagen Mutation Database |
http://www.le.ac.uk/genetics/collagen/ |
Human type I and type III collagen gene mutations |
| iARC TP53 Database |
http://www.iarc.fr/p53/ |
Human TP53 somatic and germline mutations |
| KinMutBase |
http://www.uta.fi/imt/bioinfo/KinMutBase/ |
Disease-causing protein kinase mutations |
| Mutation Spectra Database |
http://info.med.yale.edu/mutbase/ |
Mutations in viral, bacterial, yeast and mammalian genes |
| NCL Mutations |
http://www.ucl.ac.uk/ncl/ |
Mutations and polymorphisms in neuronal ceroid lipofuscinoses (NCL) genes |
| Online Mendelian Inheritance in Animals |
http://www.angis.org.au/omia |
Catalog of animal genetic and genomic disorders |
| Online Mendelian Inheritance in Man |
http://www.ncbi.nlm.nih.gov/Omim/ |
Catalog of human genetic and genomic disorders |
| PAHdb |
http://www.mcgill.ca/pahdb/ |
Mutations at the phenylalanine hydroxylase locus |
| PHEXdb |
http://data.mch.mcgill.ca/phexdb |
Mutations in PHEX gene causing X-linked hypophosphatemia |
| PMD |
http://pmd.ddbj.nig.ac.jp/ |
Compilation of protein mutant data |
| PTCH1 Mutation Database |
http://www.cybergene.se/PTCH/ptchbase.html |
Mutations and SNPs found in PTCH1 |
| RB1 Gene Mutation Database |
http://www.d-lohmann.de/Rb/ |
Mutations in the human retinoblastoma (RB1) gene |
| SV40 Large T-Antigen Mutant Database |
http://bigdaddy.bio.pitt.edu/SV40/ |
Mutations in SV40 large tumor antigen gene |
| Pathology |
|
|
| BayGenomics |
http://baygenomics.ucsf.edu |
Identification of genes relevant to cardiovascular and pulmonary disease |
| FIMM |
http://sdmc.krdl.org.sg:8080/fimm/ |
Functional molecular immunology data |
| GOLD.db |
http://gold.tugraz.at |
Genes, proteins, and pathways implicated in lipid-associated disorders |
| INFEVERS |
http://fmf.igh.cnrs.fr/infevers |
Familial Mediterranean Fever and hereditary inflammatory disorder mutation data |
| MetaFMF |
http://fmf.igh.cnrs.fr/metaFMF/index_us.html |
Familial Mediterranean Fever phenotype-genotype correlation |
| Mouse Tumor Biology Database (MTB) genetic |
http://tumor.informatics.jax.org |
Mouse tumor names, classification, incidence, pathology, genetic factors |
| Oral Cancer Gene Database |
http://www.tumor-gene.org/Oral/oral.html |
Cellular, molecular and biological data for genes involved in oral cancer |
| PEDB |
http://www.pedb.org/ |
Sequences from prostate tissue and cell type-specific cDNA libraries |
| PGDB |
http://www.ucsf.edu/PGDB |
Genes and genomic loci related to the prostate and prostatic diseases |
| Tumor Gene Family Databases (TGDBs) |
http://www.tumor-gene.org/tgdf.html |
Cellular, molecular and biological data about genes involved in various cancers |
| Protein Databases |
|
|
| AARSDB |
http://rose.man.poznan.pl/aars/index.html |
Aminoacyl-tRNA synthetase sequences |
| ABCdb |
http://ir2lcb.cnrs-mrs.fr/ABCdb/ |
ABC transporters |
| AraC/XylS database |
http://www.AraC-XylS.org |
AraC/XylS protein family of positive regulators in bacteria |
| ASPD |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ |
Artificial Selected Proteins/Peptides Database |
| CSDBase |
http://www.chemie.uni-marburg.de/~csdbase/ |
Cold shock domain-containing proteins |
| DAtA |
http://luggagefast.Stanford.EDU/group/arabprotein/ |
Annotated coding sequences from Arabidopsis |
| DExH/D Family Database |
http://www.helicase.net/dexhd/dbhome.htm |
DEAD-box, DEAH-box and DExH-box proteins |
| Endogenous GPCR List |
http://www.biomedcomp.com/GPCR.html |
G protein-coupled receptors; expression in cell lines |
| ESTHER |
http://www.ensam.inra.fr/cholinesterase/ |
Esterases and alpha/beta hydrolase enzymes and relatives |
| EXProt |
http://www.cmbi.nl/exprot |
Proteins with experimentally-verified function |
| GenProtEC |
http://genprotec.mbl.edu |
E. coli K-12 genome, gene products and homologs |
| GPCRDB |
http://www.gpcr.org/7tm/ |
G protein-coupled receptors |
| Histone Database |
http://research.nhgri.nih.gov/histones/ |
Histone and histone fold sequences and structures |
| HIV Molecular Immunology Database |
http://hiv-web.lanl.gov/immunology/ |
HIV epitopes |
| HIV RT and Protease Sequence Database |
http://hivdb.stanford.edu |
HIV reverse transcriptase and protease sequences |
| Homeobox Page |
http://www.biosci.ki.se/groups/tbu/homeo.html |
Information relevant to homeobox proteins, classification and evolution |
| Homeodomain Resource genomic |
http://research.nhgri.nih.gov/homeodomain |
Homeodomain sequences, structures and related genetic and genomic information |
| HORDE |
http://bioinfo.weizmann.ac.il/HORDE/ |
Olfactory receptor genes and proteins |
| HUGE |
http://www.kazusa.or.jp/huge/ |
Large (>50 kDa) human proteins and cDNA sequences |
| IMGT |
http://imgt.cines.fr |
Immunoglobulin, T cell receptor and MHC sequences from human and other vertebrates |
| IMGT/HLA |
http://www.ebi.ac.uk/imgt/hla/ |
Polymorphic sequences of human MHC and related genes |
| IMGT/MHC Database |
http://www.ebi.ac.uk/imgt/mhc/ |
Major histocompatibility complex sequences |
| InBase |
http://www.neb.com/neb/inteins.html |
All known inteins (protein splicing elements): properties, sequences, bibliography |
| InterPro |
http://www.ebi.ac.uk/interpro |
Protein families and domains |
| Kabat Database |
http://immuno.bme.nwu.edu/ |
Sequences of proteins of immunological interest |
| LGICdb |
http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html |
Ligand-gated ion channel subunit sequences |
| Lipase Engineering Database |
http://www.led.uni-stuttgart.de/ |
Integrated information on sequence, structure and function of lipases and esterases |
| MEROPS |
http://www.merops.ac.uk |
Proteolytic enzymes (proteases/peptidases) |
| MetaFam |
http://metafam.ahc.umn.edu/ |
Integrated protein family information |
| Metalloprotein Database and Browser |
http://metallo.scripps.edu/ |
Metal-binding sites in metalloproteins |
| MitoDrome |
http://bighost.area.ba.cnr.it/BIG/MitoDrome |
Drosophila nuclear genes encoding proteins targeted to the mitochondrion |
| MHCPEP |
http://wehih.wehi.edu.au/mhcpep/ |
MHC-binding peptides |
| MPIMP |
http://millar3.biochem.uwa.edu.au/~lister/index.html |
Mitochondrial protein import machinery of plants |
| Nuclear Protein Database (NPD) |
http://npd.hgu.mrc.ac.uk |
Proteins localized in the nucleus |
| Nuclear Receptor Resource |
http://nrr.georgetown.edu/nrr/nrr.html |
Nuclear receptor superfamily |
| NRMD |
http://www.receptors.org/NR/ |
Nuclear receptor superfamily |
| NUREBASE |
http://www.ens-lyon.fr/LBMC/laudet/nurebase.html |
Nuclear hormone receptors |
| Olfactory Receptor Database |
http://ycmi.med.yale.edu/senselab/ordb/ |
Sequences for olfactory receptor-like molecules |
| ooTFD |
http://www.ifti.org/ |
Transcription factors and gene expression |
| PANTHER |
http://panther.celera.com |
Gene products organized by biological function |
| Peptaibol |
http://www.cryst.bbk.ac.uk/peptaibol/welcome.html |
Peptaibol (antibiotic peptide) sequences |
| PhosphoBase |
http://www.cbs.dtu.dk/databases/PhosphoBase/ |
Protein phosphorylation sites |
| PIR-NREF |
http://pir.georgetown.edu/pirwww/pirnref.shtml |
Non-redundant reference database with comprehensive protein sequences |
| PKR |
http://pkr.sdsc.edu |
Protein kinase sequences, enzymology, genetics and molecular and structural properties |
| PLANT-PIs |
http://bighost.area.ba.cnr.it/PLANT-PIs |
Plant protease inhibitors |
| PlantsP/PlantsT |
http://plantsp.sdsc.edu |
Functional geomics databases focusing on protein involved in plant phosphorylation and membrane transport, respectively |
| PPMdb data |
http://sphinx.rug.ac.be:8080/ppmdb/index.html |
Arabidopsis plasma membrane protein sequence and expression data |
| Prolysis |
http://delphi.phys.univ-tours.fr/Prolysis/ |
Proteases and natural and synthetic protease inhibitors |
| Protein Information Resource (PIR) |
http://pir.georgetown.edu |
Comprehensive, annotated, non-redundant protein sequence databases |
| ProtoNet |
http://www.protonet.cs.huji.ac.il/ |
Hierarchical clustering of SWISS-PROT |
| Ribonuclease P Database |
http://www.mbio.ncsu.edu/RNaseP/home.html |
RNase P sequences, alignments and structures |
| RTKdb |
http://pbil.univ-lyon1.fr/RTKdb/ |
Receptor tyrosine kinase sequences |
| S/MARt dB |
http://transfac.gbf.de/SMARtDB/ |
Nuclear scaffold/matrix attached regions |
| SDAP |
http://fermi.utmb.edu/SDAP |
Sequences, structures and IgE epitopes of allergenic proteins |
| SENTRA |
http://wit.mcs.anl.gov/WIT2/Sentra/HTML/sentra.html |
Sensory signal transduction proteins |
| SEVENS |
http://sevens.cbrc.jp |
7-transmembrane helix receptors |
| SRPDB |
http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html |
Structural and functional information on signal recognition particles |
| SWISS-PROT/TrEMBL |
http://www.expasy.ch/sprot |
Curated protein sequences |
| TIGRFAMs |
http://www.tigr.org/TIGRFAMs |
Functional identification of proteins |
| TRANSFAC |
http://transfac.gbf.de/TRANSFAC/index.html |
Transcription factors and binding sites |
| trEST, trGEN, Hits |
http://hits.isb-sib.ch |
Hypothetical protein sequences |
| VIDA |
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html |
Homologous viral protein families |
| Wnt Database |
http://www.stanford.edu/~rnusse/wntwindow.html |
Wnt proteins and phenotypes |
| Protein Sequence Motifs |
|
|
| ASC—Active Sequence Collection |
http://crisceb.unina2.it/ASC/ |
Biologically-active short amino acid sequences |
| Blocks |
http://blocks.fhcrc.org |
Multiple alignments of conserved regions of protein families |
| CDD |
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml |
Alignment models for conserved protein domains |
| CluSTr |
http://www.ebi.ac.uk/clustr/ |
Automatic classification of SWISS-PROT+TrEMBL proteins |
| eMOTIF |
http://motif.stanford.edu/emotif |
Protein sequence motif determination and searches |
| InterPro domains |
http://www.ebi.ac.uk/interpro/ |
Integrated documentation resource for protein families, domains, and sites |
| iProClass |
http://pir.georgetown.edu/iproclass/ |
Annotated protein database with family, function and structure information |
| NESbase 1.0 |
http://www.cbs.dtu.dk/databases/NESbase |
Nuclear export signals |
| NLSdb |
http://cubic.bioc.columbia.edu/db/NLSdb/ |
Nuclear localization signals |
| O-GLYCBASE |
http://www.cbs.dtu.dk/databases/OGLYCBASE/ |
O- and C-linked glycosylation sites in proteins |
| Pfam |
http://www.sanger.ac.uk/Software/Pfam/ |
Multiple sequence alignments and hidden Markov models of common protein domains |
| PIR-ALN |
http://pir.georgetown.edu/pirwww/dbinfo/piraln.html |
Protein sequence alignments |
| PRINTS |
http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ |
Hierarchical gene family fingerprints |
| ProClass patterns |
http://pir.georgetown.edu/gfserver/proclass.html |
Protein families defined by PIR superfamilies and PROSITE patterns |
| ProDom |
http://www.toulouse.inra.fr/prodom.html |
Protein domain families |
| PROSITE |
http://www.expasy.org/prosite |
Biologically-significant protein patterns and profiles |
| ProtoMap |
http://protomap.cornell.edu |
Automated hierarchical classification of SWISS-PROT proteins |
| SBASE |
http://www.icgeb.org/sbase |
Protein domain sequences and tools |
| SMART |
http://smart.embl-heidelberg.de |
Simple Modular Architecture Research Tool |
| SUPFAM |
http://pauling.mbu.iisc.ernet.in/~supfam |
Grouping of sequence families into superfamilies |
| SYSTERS, GeneNest, SpliceNest |
http://cmb.molgen.mpg.de |
Integrated database of protein families, EST clusters and their genomic positions |
| TMPDB |
http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/ |
Experimentally-characterized transmembrane topologies |
| Proteome Resources |
|
|
| AAindex |
http://www.genome.ad.jp/aaindex/ |
Physicochemical and biological properties of amino acids |
| GELBANK |
http://gelbank.anl.gov |
2D-gel electrophoresis patterns from completed genomes |
| PEP: Predictions for Entire Proteomes |
http://cubic.bioc.columbia.edu/pep/ |
Summarized analyses of protein sequences |
| Proteome Analysis Database |
http://www.ebi.ac.uk/proteome/ |
Online application of InterPro and cluSTr for the functional classification of proteins in whole genomes |
| REBASE |
http://rebase.neb.com/rebase/rebase.html |
Restriction enzymes and associated methylases |
| SWISS-2DPAGE |
http://www.expasy.org/ch2d/ |
Annotated two-dimensional polyacrylamide gel electrophoresis database |
| Retrieval Systems and Database Structure |
|
|
| TESS |
http://www.cbil.upenn.edu/tess |
Transcription element search system |
| Virgil |
http://www.infobiogen.fr/services/virgil |
Database interconnectivity |
| RNA Sequences |
|
|
| 16S and 23S Ribosomal RNA Mutation Database |
http://www.fandm.edu/Departments/Biology/Databases/RNA.html |
16S and 23S ribosomal RNA mutations |
| 5S Ribosomal RNA Database |
http://biobases.ibch.poznan.pl/5SData/ |
5S rRNA sequences |
| ACTIVITY |
http://util.bionet.nsc.ru/databases/activity.html |
Functional DNA/RNA site activity |
| ARED |
http://rc.kfshrc.edu.sa/ared |
AU-rich element-containing mRNAs |
| Database for mobile group II introns |
http://www.fp.ucalgary.ca/group2introns/ |
Database for mobile group II introns |
| Guide RNA Database |
http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html |
Guide RNA sequences |
| HyPaLib |
http://bibiserv.techfak.uni-bielefeld.de/HyPa/ |
Structural elements characteristic for classes of RNA |
| Intronerator |
http://www.cse.ucsc.edu/~kent/intronerator/ |
RNA splicing and gene structure in C. elegans; alignments of C. briggsae and C. elegans genomic sequences |
| IRESdb |
http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ |
Internal ribosome entry sites |
| NCIR |
http://prion.bchs.uh.edu/bp_type/ |
Non-standard base-base interactions in known RNA structures |
| Noncoding regulatory RNAs database |
http://biobases.ibch.poznan.pl/ncRNA/ |
Noncoding RNAs with regulatory functions |
| PLANTncRNAs |
http://www.prl.msu.edu/PLANTncRNAs/ |
Plant non-protein coding RNAs with relevant gene expression information |
| Plant snoRNA DB |
http://www.scri.sari.ac.uk/plant_snoRNA/ |
snoRNA genes in plant species |
| PLMItRNA |
http://bighost.area.ba.cnr.it/PLMItRNA/ |
Mitochondrial tRNA genes and molecules in photosynthetic eukaryotes |
| PseudoBase |
http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html |
Structural, functional and sequence data related to RNA pseudoknots |
| Rfam |
http://www.sanger.ac.uk/Software/Rfam/ |
Non-coding RNA families |
| Ribosomal Database Project (RDP-II) |
http://rdp.cme.msu.edu |
rRNA sequence data, analysis tools, alignments and phylogenies |
| RISCC |
http://ulises.umh.es/RISSC |
Ribosomal 16S–23S RNA gene spacer regions |
| RNA Modification Database |
http://medlib.med.utah.edu/RNAmods/ |
Naturally modified nucleosides in RNA |
| SELEXdb |
http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ |
Selected DNA/RNA functional site sequences |
| Small RNA Database |
http://mbcr.bcm.tmc.edu/smallRNA |
Direct sequencing of small RNA sequences from prokaryotes and eukaryotes |
| SRPDB |
http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html |
Signal recognition particle RNA, SRP protein and SRP receptor sequences and alignments |
| Subviral RNA Database |
http://penelope.med.usherb.ca/subviral/ |
Database of viroids and viroid-like RNAs |
| tmRDB |
http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html |
tmRNA (10Sa RNA) sequences and alignments |
| tRNA Sequences |
http://www.uni-bayreuth.de/departments/biochemie/trna/ |
tRNA and tRNA gene sequences |
| tmRNA Website |
http://www.indiana.edu/~tmrna |
tmRNA sequences, foldings, and alignments |
| UTRdb/UTRsite |
http://bighost.area.ba.cnr.it/srs6/ |
5'- and 3'-UTRs of eukaryotic mRNAs and relevant functional patterns |
| Yeast snoRNA Database |
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html |
Yeast small nucleolar RNAs |
| Structure |
|
|
| ASTRAL |
http://astral.stanford.edu/ |
Sequences of domains of known structure, selected subsets and sequence-structure correspondences |
| BioMagResBank acids |
http://www.bmrb.wisc.edu/ |
NMR spectroscopic data from proteins peptides, and nucleic acids |
| CADB |
http://144.16.71.148 |
Conformation angles of protein structures, with associated crystallographic data |
| CATH |
http://www.biochem.ucl.ac.uk/bsm/cath_new |
Protein domain structures |
| CE |
http://cl.sdsc.edu/ce.html |
CE: a resource to compute and review 3D protein structure alignments |
| CKAAPs DB |
http://ckaap.sdsc.edu |
Structurally-similar proteins with dissimilar sequences |
| CSD |
http://www.ccdc.cam.ac.uk/prods/csd/csd.html |
Crystal structure information for organicand metal organic compounds |
| Database of Macromolecular Movements |
http://bioinfo.mbb.yale.edu/MolMovDB/ |
Descriptions of protein and macromolecular motions, including movies |
| Decoys ‘R’ Us |
http://dd.stanford.edu/ |
Computer-generated protein conformations based on sequence data |
| DSDBASE |
http://www.ncbs.res.in/%7Efaculty/mini/dsdbase/dsdbase.html |
Native and modeled disulfide bonds in proteins |
| DSMM |
http://projects.eml.org/mcm/database/dsmm |
Database of Simulated Molecular Motions |
| E-MSD |
http://www.ebi.ac.uk/msd |
Collected data on macromolecular structures |
| FAMSBASE |
http://famsbase.bio.nagoya-u.ac.jp/famsbase/ |
Protein three-dimensional structural models |
| Gene3D |
http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/ |
Precalculated structural assignments for genes within whole genomes |
| GTOP |
http://spock.genes.nig.ac.jp/~genome/gtop.html |
Protein fold predictions from genome sequences |
| HIC-Up |
http://alpha2.bmc.uu.se/hicup/ |
Structures of small molecules (‘hetero-compounds’) |
| HSSP |
http://www.sander.ebi.ac.uk/hssp/ |
Structural families and alignments; structurarlly-conserved regions and domain architecture |
| IMB Jena Image Library of Biological Macromolecules |
http://www.imb-jena.de/IMAGE.html |
Visualization and analysis of three-dimensional biopolymer structures |
| ISSD |
http://www.protein.bio.msu.su/issd/ |
Integrated sequence and structural information |
| LPFC |
http://www-smi.stanford.edu/projects/helix/LPFC/ |
Library of protein family core structures |
| MMDB linked |
http://www.ncbi.nlm.nih.gov/Structure/ |
All experimentally-determined three-dimensional structures, linked to NCBI Entrez |
| MolMovDB |
http://MolMovDB.org |
Database of macromolecular movements |
| ModBase |
http://guitar.rockefeller.edu/modbase |
Annotated comparative protein structure models |
| NDB |
http://ndbserver.rutgers.edu/ |
Nucleic acid-containing structures |
| NTDB |
http://ntdb.chem.cuhk.edu.hk |
Thermodynamic data for nucleic acids |
| PALI |
http://pauling.mbu.iisc.ernet.in/~pali |
Phylogeny and alignment of homologous protein structures |
| PASS2 |
http://ncbs.res.in/%7Efaculty/mini/campass/pass.html |
Structural motifs of protein superfamilies |
| PDB |
http://www.pdb.org/ |
Structure data determined by X-ray crystallography and NMR |
| PDB-REPRDB |
http://www.cbrc.jp/pdbreprdb/ |
Representative protein chains, based on PDB entries |
| PDBsum |
http://www.biochem.ucl.ac.uk/bsm/pdbsum |
Summaries and analyses of PDB structures |
| PRESAGE |
http://presage.berkeley.edu/ |
Protein structures with experimental and predictive annotations |
| ProTherm |
http://www.rtc.riken.go.jp/jouhou/protherm/protherm.html |
Thermodynamic data for wild-type and mutant proteins |
| PSSH |
http://srs3d.ebi.ac.uk/ |
Alignments between protein sequences and tertiary structures |
| RESID |
http://www-nbrf.georgetown.edu/pirwww/dbinfo/resid.html |
Protein structure modifications |
| RNABase |
http://www.rnabase.org |
RNA-containing structures from PDB and NDB |
| SCOP |
http://scop.mrc-lmb.cam.ac.uk/scop |
Familial and structural protein relationships |
| SCOR |
http://scor.lbl.gov |
RNA structural relationships |
| Sloop |
http://www-cryst.bioc.cam.ac.uk/~sloop/ |
Classification of protein loops |
| Structure-Superposition Database |
http://ssd.rbvi.ucsf.edu |
Pairwise superposition of TIM-barrel structures |
| SUPERFAMILY |
http://supfam.org |
Assignments of proteins to structural superfamilies |
| Transgenics |
|
|
| Cre Transgenic Database |
http://www.mshri.on.ca/nagy/cre.htm |
Cre transgenic mouse lines |
| Transgenic/Targeted Mutation Database |
http://tbase.jax.org/ |
Information on transgenic animals and targeted mutations |
| Varied Biomedical Content |
|
|
| BAliBASE alignments |
http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html |
Benchmark database for comparison of multiple sequence alignments |
| Cytokine Gene Polymorphism in Human Disease |
http://bris.ac.uk/pathandmicro/services/GAI/cytokine4.htm |
Cytokine gene polymorphism literature database |
| DBcat |
http://www.infobiogen.fr/services/dbcat/ |
Catalog of databases |
| Global Image Database |
http://www.gwer.ch/qv/gid/gid.htm |
Annotated biological images |
| GlycoSuiteDB |
http://www.glycosuite.com |
N- and O-linked glycan structures and biological source information |
| Imprinted Genes and Parent-of-Origin Effects |
http://www.otago.ac.nz/IGC |
Imprinted genes and parent-of-origin effects in animals |
| MPDB |
http://www.biotech.ist.unige.it/interlab/mpdb.html |
Information on synthetic oligonucleotides proven useful as primers or probes |
| NCBI Taxonomy Browser |
http://www.ncbi.nlm.nih.gov/Taxonomy/ |
Names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence |
| probeBase |
http://www.probeBase.net |
rRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information |
| PubMed |
http://www.ncbi.nlm.nih.gov/PubMed/ |
MEDLINE and Pre-MEDLINE citations |
| RefSeq |
http://www.ncbi.nlm.nih.gov/LocusLink/refseq.html |
Reference sequence standards for genomes, genes, transcripts and proteins |
| RIDOM |
http://www.ridom.de/ |
rRNA (16S and ITS) sequence-based identification of medical microorganisms |
| SWEET-DB |
http://www.dkfz-heidelberg.de/spec2/sweetdb/ |
Annotated carbohydrate structure and substance information |
| The Pharmacogenomics and PharmacogeneticsKnowledge Base |
http://www.pharmgkb.org |
Variation in drug response based on human variation |
| Tree of Life |
http://phylogeny.arizona.edu/tree/phylogeny.html |
Information on phylogeny and biodiversity |
| Vectordb |
http://www.atcg.com/vectordb/ |
Characterization and classification of nucleic acid vectors |
| VirOligo |
http://viroligo.okstate.edu |
Virus-specific oligonucleotides for PCR and hybridization |
|
