Gene Data base Publications

Molecular Biology Database abbrebiations for Publications

In Publications you ofter will find references of old Databases. Now most databases are absorbed in BLAST and NCBI.

However some of these database contain unique sequence alignments.

16S and 23S rRNA Mutation Database16S and 23S ribosomal RNA mutations
2D-PAGEProteome database system for microbial research
3D rRNA modification mapsLocations of modified rRNA nucleotides within the 3D structure of the ribosome
3D-GenomicsStructural annotations for complete proteomes
3DID3D interacting domains
3DID3D interacting domains: Domain-domain interactions in proteins with known 3D structures
3D-InterologsProtein-protein interactions in various evolutionary lineages
4DXpressDatabase for cross species expression pattern comparisons
5S rRNA Database5S rRNA sequences
5’SAGE5′-end serial analysis of gene expression
AAindexPhysicochemical properties of amino acids
AANTAmino Acid – Nucleotide interaction database
ABAAscidian body atlas: digital 3D model of ascidian development
ABCdbArchaeal and bacterial ABC transporter database
ABSAnnotated regulatory binding sites from orthologous promoters
ACeDBC. elegans, S. pombe, and human genomic information
ACLAMEA classification of genetic mobile elements
ACTIVITYFunctional DNA/RNA site activity
ADDADatabase of protein domain classification
AffinDBAffinity data for protein-ligand complexes
AgBaseGO annotations for agriculturally important plants and animals
AGDAshbya gossypii genome database
AGNSArabidopsis GeneNet supplementary
AGRISArabidopsis gene regulatory information server
ALFREDAllele frequencies and DNA polymorphisms
AllGenesHuman and mouse gene, transcript and protein annotation
ALPSbaseAutoimmune lymphoproliferative syndrome database
AlterORFDatabase of alternate open reading frames
AlzGeneCandidate genes for Alzheimer disease
aMAZEA system for the annotation, management, and analysis of biochemical and signalling pathway networks
Aminoacyl-tRNA synthetases databaseAminoacyl-tRNA synthetase database
AMPDBArabidopsis Mitochondrial Protein Database
Androgen Receptor Gene Mutations DBMutations in the androgen receptor gene
AngioDBDatabase of angiogenesis and angiogenesis-related molecules
Animal Genome Size DatabaseGenome sizes of vertebrates and invertebrates
Animal Toxin DBDatabase of animal toxins
AnimalQTLdbQuantitative trait loci in livestock animals
AntiJenQuantitative binding data for peptides and proteins of immunological interest
ANTIMICDatabase of natural antimicrobial peptides
AOBaseAntisense oligonucleotide selection and design
APDAntimicrobial Peptide Database
AphidBaseGenomic database for the pea aphid (Acyrthosiphon pisum)
ApiDBUnified resource for various apicomplexan species
ApiDotsEST sequences from various Apicomplexan parasites
AppaDBDatabase on the nematode Pristionchus pacificus
Aptamer DatabaseSmall RNA/DNA molecules binding nucleic acids, proteins
Arabidopsis MPSSArabidopsis gene expression detected by massively parallel signature sequencing
Arabidopsis Nucleolar Protein DatabaseComparative analysis of human and Arabidopsis nucleolar proteomes
Arabidopsis Small RNA ProjectArabidopsis Small RNA sequences
ARAMEMNONArabidopsis thaliana membrane proteins and transporters
ArchDBAutomated classification of protein loop structures
AREDAU-rich element-containing mRNAs
ArgonauteGene regulation by mammalian microRNAs
ArkDBGenome databases for farm and other animals
ArrayExpressPublic collection of microarray gene expression data
ARTADEdbArabidopsis tiling-array-based detection of exons
ASAPA Systematic Annotation Package
ASAP IIComparative analysis of alternative splicing in animal species
ASCActive Sequence Collection
ASDBAlternative Splicing Database: protein products and expression patterns of alternatively-spliced genes
ASHESdbAlternatively Spliced Human genes by Exon Skipping
ASPDArtificial selected proteins/peptides database
ASTDAlternative Splicing and Transcript Diversity database
ASTRALSequences of domains of known structure, selected subsets and sequence-structure correspondences
ATDAlternate transcript diversity databaseSuperseded by ASTD, no. 28
AtGDBArabidopsis thaliana genome database
AthaMapGenome-wide map of putative transcription factor binding sites in Arabidopsis thaliana
Atlas of Genetics and Cytogenetics in Onco-logy and HaematologyCancer related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseases
AtPIDArabidopsis thaliana Protein Interactome Database
ATTED-IICoexpressed gene sets and gene regulators in Arabidopsis
AutoPSIAutomated structural classification of protein sequences
AxeldbGene expression in Xenopus laevis
BacMapPicture atlas of annotated bacterial genomes
BacMapPicture atlas of annotated bacterial genomes
Bacteriome.orgProtein interaction database for E. coli
BACTIBASEDatabase of bacteriocin natural antimicrobial peptides
BacTregulatorsTranscriptional regulators of AraC and TetR familiesNo longer maintained
BAliBASEBenchmark database for comparison of multiple sequence alignments
BANMOKIDatabase of bacterial nucleoside monophosphate kinases
BarleyBaseExpression profiling of plant genomes
BayGenomicsPublicly available mouse gene trap cell linesSuperseded by Gene Trap database, no. 827
BCIpepDatabase of B-cell epitopes
BCSDB/GlycoscienceBacterial Carbohydrate Structure DataBase
BeetleBaseGenome database of the beetle Tribolium castaneum
BenchmarkProtein classification benchmark collection: training/test sets for machine learning
BGEDBrain Gene Expression Database
BGI-RISeBeijing Genomics Institute Rice Information System
BINDBiomolecular interaction network databaseNo longer free for all
Binding MOADBinding Mother of All Databases: protein-ligand crystal structures
BindingDBBinding affinities of protein-ligand and other complexes
BioCartaOnline maps of metabolic and signaling pathways
BioCartaOnline maps of metabolic and signaling pathways
BioCycPathway/genome databases for many bacteria
Biodefense Proteomics Resource CenterProteomics and host-pathogen interactions for biodefense-related microorganisms
Biodegradative Strain DatabaseMicroorganisms that can degrade aromatic and other organic compounds
BioGRIDGenetic and physical interactions in yeast, worm and fly
BioHealthBaseHost-pathogen interactions of influenza virus
BioImageDatabase of multidimensional biological images
BioMagResBankNMR spectroscopic data from proteins, peptides, and nucleic acids
BioModelsPublished mathematical models of biological interest
BioSilicoIntegrated access to various metabolic databases
BioThesaurusA collection of gene/protein names and associated sequences
BIOZONDatabase of gene and protein familiy classification
BlocksAlignments of conserved regions in protein families
BodyMapHuman and mouse gene expression data
BodyMap-XsCross-species comparison of vertebrate gene expression
Brassica BASCDatabase for Brassica genomic research
BRENDAEnzyme names and biochemical properties
BRITEBiomolecular Relations in Information Transmission and Expression
BSORFBacillus subtilis Open Reading Frames
BTKbaseMutation registry for X-linked agammaglobulinemia
BuchneraBaseGenomic database for the pea aphid symbiont Buchnera sp. APS
ButterflyBaseGenomics of butterflies (Lepidoptera)
C. elegans ProjectGenome sequencing data at the Sanger Institute
CADBConformational Angles DataBase of Proteins
CADRECentral Aspergillus data repository
CAGECAGE tags for cap-analysis of gene expression
CampyDBCampylobacter DatabaseIncoroporated into xBase, no. 426
Cancer ChromosomesCytogenetic, clinical, and reference information on cancer-related aberrations
CancerGenesGene selection resource for cancer genome projects
Candida GenomeCandida albicans genome database
CandidaDBCandida albicans genome database
CanGEMGene copy number changes in cancer
CarbBankCCSD – Complex Carbohydrate Structure Database
CarpeDBComprehensive database on the genetics of epilepsy
CASRDBCalcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidism
CATdbArabidopsis transcriptome data
CATHProtein domain structures database
CATMAComplete Arabidopsis Transcriptome MicroArray
CCDBCyberCell Database
CDDConserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases
CECombinatorial Extension method to compute and review 3D protein structure alignments
CEBSDatabase of toxicogenomics, microarray and proteomics data.
CellCircuitsMolecular network models: from pairwise molecular interactions to whole pathways
Cereal Small RNA DBSmall RNAs expressed in rice and maize
CFGPComparative Fungal Genomics Platform
CGEDCancer Gene Expression Database
ChEBIChemical entities of biological interest
ChemBankStructures and biological activities of small organic molecules
ChemDB3D structures and properties of small molecules
ChickVDSequence variation in the chicken genome
ChimerDBChimeric (fusion) sequences in human, rat and mouse
Chloroplast genome DBChloroplast genome database
ChromDBChromatin-associated proteins in a broad range of organisms
CIDBChlamydia Interactive Database: Gene expression data
Ciliate IES-MDS DbMacro- and micronuclear genes in spirotrichous ciliates
CisRedHuman regulatory DNA sequence motifs
CKAAPs DBConserved Key Amino Acid Positions DatabaseNo longer maintained
CleanExExpression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons
ClostriDBClostridium DatabaseIncoroporated into xBase, no. 426
CluSTrClusters of UniProt Knowledgebase and IPI proteins
CMGSDBComputational models for gene silencing in C. elegans
CnidBaseCnidarian evolution and gene expression database
CoC CentralUniversally conserved residues in protein folds
COGClusters of orthologous groups of proteins
COGEMEPhytopathogenic fungi and oomycete EST database
CoGenT++Complete genome tracking: Predicted peptides from fully sequenced genomes
coliBaseDatabase for E. coli, Salmonella and Shigella
ColiSNPMapping non-synonymous SNPs on protein structures
Collagen Mutation DBHuman type I and type III collagen gene mutations
ColumbaAnnotation of protein structures from the PDB
COMeCo-Ordination of Metals etc.
ComparasiteDatabase for comparative study of parasite cDNAs
Comparative GenometricsDNA walks, nucleotide skews and other biometric measures of prokaryotic genomes
Consensus CDSCollaborative effort to identify a core set of human proteins
CoPSComprehensive peptide signature database
CORGComparative Regulatory Genomics: conserved non-coding blocks in vertebrate species
CORGCOmparative Regulatory Genomics: conserved non-coding blocks
CORUMExperimentally verified mammalian protein complexes
CoryneRegNetCorynebacterial transcription factors
COSMICCatalogue Of Somatic Mutations In Cancer: Sequence data, samples and publications
CoVDBDatabase of coronavirus genes and genomes
COXPRESdbCoexpressed genes and networks in human and mouse
cpnDBChaperonin database
Cre Transgenic DBCre transgenic mouse lines with links to publications
CREMOFACDatabase of chromatin remodeling factors
CR-ESTCropp ESTs: Barley, wheat, pea, and potato ESTs
CryptoDBCryptosporidium database
CSACatalytic Site Atlas
CSDCambridge Structural Database
CSDBaseCold Shock Domain database
CSSCarbohydrate Structure Suite: carbohydrate 3D structures
CTCF Binding Site DBExperimentally identified and predicted CTCF binding sites
CTGADatabase for genetic disorders in Arabs
CutDBCommunity annotation resource for proteases, their substrates and cleavage sites
CUTGCodon Usage Tabulated from GenBank
CuticleDBStructural proteins of Arthropod cuticle
CyanoBaseCyanobacterial genomes
CyBaseProteins with cyclic backbones
CycleBaseGene expression profiles from cell-cycle microarray studies
CyclonetDatabase on cell cycle regulation
CYGDMIPS Comprehensive yeast genome database
CyMoBaseCytoskeletal and motor proteins database
Cypriot national mutation databaseDisease mutations in the Cypriot population
Cytokine Gene Poly-morphism DatabaseCytokine gene polymorphism literature database
Dali databaseFold classification based on structural alignment of proteins
DARTDrug Adverse Reaction Targets
Database of Genomic VariantsHuman genomic variants: frequency, segmental duplications and genome assembly gaps
Database of Germline p53 MutationsMutations in human tumor and cell line p53 gene
DATFDatabase of Arabidopsis transcription factors
DBAliDatabase of structure alignments
DBDTranscription factor prediction database
dbERGEIIDatabase of experimental results on gene expression: Genomic alignment, annotation and experimental data
dbLEPDatabase of Liver proteome expression profiles
dbMHCGenetic and clinical database of the human MHC
DB-PABPExperimentally characterized polyanion-binding proteins
dbPTMInformation on post-translational modification of proteins
dbQSNPQuantification of SNP allele frequencies database
dbRESDatabase of known RNA editing sites
dbRIPHuman retrotransposon insertion polymorphism
dbSNPDatabase of single nucleotide polymorphisms
DBSubLoc –Database of protein Subcellular Localization
DBTBSBacillus subtilis promoters and transcription factors
DBTBSBacillus subtilis promoters and transcription factors
DBTGRDatabase of tunicate Ciona gene regulation
DBTSSDatabase of transcriptional start sites
DCCPDatabase of Copper-Chelating Proteins
DDBJ – DNA Data Bank of JapanAll known nucleotide and protein sequences
DDIBDatabase of domain interactions and binding
Decoys-R-UsComputer-generated protein conformations based on sequence data
DEDDatabase of evolutionary distancesNo longer maintained
Defensins KnowledgebaseAntimicrobial peptides of the defensin family
DEGDatabase of Essential Genes
Déjà vuDuplicate citations in the scientific literature
DENIZBeta-thalassemia allele frequencies in world populationsNo longer maintained
DExH/D Family DBDEAD-box, DEAH-box and DExH-box proteins
DG-CSTDisease gene conserved sequence tagshttp://
D-HaploDBDefinitive haplotype database
diArkDatabase of eukaryotic sequencing projects
Diatom EST DBESTs from diatom algae Thalassiosira and Phaeodactylum
DictyBaseUniversal resource for Dictyostelium discoideum
DIMADomain interaction map: experimental data and predictions on protein domain interactions
DIPDatabase of interacting proteins: Experimentally-determined protein-protein interactions
DisProtDatabase of Protein Disorder
DMAPSDatabase of multiple alignments for protein structures
DockgroundProtein-protein interfaces in co-crystallized protein structures
DOMINEKnown and predicted protein domain interactions in PDB entries
DOMINODomain peptide interactions
DomInsDatabase of Domain Insertions
DoOPDatabases of Orthologous Promoters: chordates and plants
DPDBDrosophila polymorphism database
DPInteractBinding sites for E. coli DNA-binding proteins
DPVwebDescriptions of plant viruses
DRASTICDatabase resource for analysis of signal transduction in plant cells
DRCDatabase of ribosomal crosslinks
DroIDDrosophila gene and protein interaction data
Drosophila microarray centreCanadian Drosophila microarray centre
DroSpeGeDrosophila Species Genomes
DRTFDatabase of Rice Transcription Factors
DrugBankCombined information on drugs and drug targets
DSDDatabase of dehydrogenase stereospecificities
DSDBASEDisulfide Database
DSMMA Database of Simulated Molecular Motions
DynaProt 2DProteome database of Lactococcus lactis
EASEDExtended Alternatively Spliced EST Database
EBI GenomesEBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
eBLOCKSHighly conserved protein sequence blocks
ECgeneGenome annotation for alternative splicing
EchoBASEPost-genomic studies of Escherichia coli
EcoCycE. coli K12 genes, pathways, transporters, and gene regulation
EcoGeneSequence and literature data on E. coli genes and proteins
ECRbaseDatabase of Evolutionary Conserved Regions, promoters, and transcription factor binding sites
EDASEST-derived alternative splicing database
Edinburgh Mouse AtlasDigital atlas of mouse embryonic development
eF-siteElectrostatic surface of Functional site
eggNOGEvolutionary genealogy of genes: Non-supervised Orthologous Groups
EGOEukaryotic Gene Orthologs
EHCOEncyclopedia of hepatocellular carcinoma genes online
EICO DBExpression-based Imprint Candidate Organiser
EIDExon-intron database
EMAGEEdinburgh mouse atlas gene expression database
EMBL Nucleotide Sequence DatabaseAll known nucleotide and protein sequences
EMGlibEnhanced microbial genomes library: Completely sequenced genomes of unicellular organisms
eMOTIFProtein sequence motif determination and searches
E-MSDEBI-Macromolecular Structure Database
ENCODE ProjectEncyclopedia of DNA Elements, all functional elements in the human genome
Endogenous GPCR ListG protein-coupled receptors; expression in cell lines
EndoNetInformation on endocrine networks
EnsemblAnnotated information on eukaryotic genomes
Entrez GeneGene-centered information at NCBI
Entrez GenomesNCBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
ENZYMEEnzyme nomenclature and properties
Enzyme NomenclatureIUBMB Nomenclature Committee recommendations
EPConDBGene expression in pancreatic development, beta cell function and diabetes
EPDEukaryotic promoter database
EPGDEukaryotic Paralog Group Database
EpitomeAntigenic epitopes in proteins and antibodies that bind them
EpoDBGenes expressed during human Erythropoiesis database
ERGDBEstrogen Responsive Genes Database
ERGO-LightIntegrated biochemical data on 10 bacterial genomes: Publicly-available portion of the ERGO database
ERICEnteropathogen Resource Integration Center
EROP-MoscowDatabase of Endogenous Regulatory OligoPeptides
eSLDBeukaryotic proteins Subcellular Localization Database
Essential genes in E. coliA list of genes essential for viability of E. coli
ESTHEREsterases and other alpha/beta hydrolase enzymes
euGenesGenomic Information for Eukaryotic Organisms
euHCVdbEuropean Hepatitis C Virus database
European rRNA DBAll complete or nearly complete rRNA sequences
EuroPhenomeLarge-scale phenotyping of knockout mouse lines
EVERESTAutomatically generated protein domain families
EvolaHuman genes and their vertebrate orthologs
ExIntExon–intron structure of eukaryotic genes
EXProtSequences of proteins with experimentally verified function
ExtraTRAINExtragenic regions and transcriptional regulators in bacteria and archaea
EyeSiteFamilies of proteins functioning in the eye
EzCatDBEnzyme Catalytic Mechanism Database
FANTOMFunctional annotation of mouse full-length cDNA clones
FCPFunctional coverage of the proteome by structures
FESDFunctional Element SNPs Database: SNPs located within promoters, UTRs, etc., of human genes
FESDFunctional Element SNPs Database: SNPs located within promoters, UTRs, etc., of human genes  
FGDBMIPS Fusarium graminearum genome database
FIMMFunctional molecular immunology data
FINDBaseFrequencies of INherited Disorders
FireDBFunctionally important residues in protein structures
FLAGdb++Integrative database about plant genomes
FLIGHTDrosophila phenotypes, gene expression and protein interactions
FLJ-DBAnnotated full-length human cDNAs (formerly HUNT database)
FlyBaseDrosophila sequences and genomic information
FlyBrainDatabase of the Drosophila nervous system
FlyMineIntegration of insect genomic and proteomic data
FlyRNAi DRSCGenome-wide RNAi analysis data in Drosophila
FLYSNPSingle nucleotide polymorphism data for Drosophila melanogaster
FlyTFDrosophila Transcription Factors
FlyTrapDrosophila mutants created using protein trap strategy
FlyViewDrosophila development and genetics
ForestTreeDBAnnotated ESTs from diverse organs of conifer and poplar trees
FREPFunctional Repeats in mouse cDNAs
fRNAdbFunctional RNA Database: noncoding transcripts that affect gene expression
FSNFlexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool
F-SNPFunctional effects of various human SNPs
FSSPSuperseded by the Dali database, no. 442 
FUGOIDFunctional genomics of organelle introns database
Full-MalariaFull-length cDNA library from erythrocytic-stage Plasmodium
Fungal Genome Size DatabaseGenome sizes of various fungi
FUNPEPLow-complexity peptides capable of forming amyloid plaque
FunShiftFunctional divergence between the subfamilies of a protein domain family
FunSimMatGene Ontology-based functional similarity values for proteins and protein families
FusionDBDatabase of bacterial and archaeal gene fusion events
GABI-KatFlanking sequence tags for T-DNA insertions in Arabidopsis
GabiPDCentral database of the German Plant Genome Project
GadFlyGenome annotation database of Drosophila
GALAGenomic alignment, annotation and experimental results
Gallus GbrowseGenomic information on chicken and other avian species
GDBHuman genes and genomic maps
GEISHAGallus expression in situ hybridization analysis
GELBANK2D gel electrophoresis patterns of proteins from complete microbial genomes
GenAtlasHuman genes, markers and phenotypes
GenBank®All known nucleotide and protein sequences
GenDiSGenomic distribution of protein structural superfamilies
Gene Aging NexusAging-related gene expression data
Gene Expression in Tooth DatabaseGene expression in dental tissue
Gene Resource LocatorAlignment of ESTs with finished human sequenceNo longer maintained
Gene3DPrecalculated structural assignments for whole genomes
GeneAnnotRevised annotation of Affymetrix human gene probe sets
GeneCardsIntegrated database of human genes, maps, proteins and diseases
GeneDBCurated database for various Sanger-sequenced genomes
GeneFarmExpert annotation of Arabidopsis gene and protein families
GeneLocGene location database
GeneNestGene indices of human, mouse, zebrafish, etc.
GeneNetDatabase on gene network components
GeneNoteHuman genes expression profiles in healthy tissues
GenePaintGene expression patterns in the mouse
GeneSpeedProtein domains in the expressed human, mouse, fly and worm genes
Genetic CodesGenetic codes in various organisms and organelles
Genetics Home ReferenceA general guide on human hereditary diseases
GeneTideA transcriptome-focused member of the GeneCards suite
GeneTrapExpression patterns in an embryonic stem library of gene trap insertions
GeneTreesPre-compiled alignments and gene phylogenies for a variety of taxonomic groups
GeniSysEnhancer- and promoter-inserted mutants of Drosophila
GenMapDBMapped human BAC clones
GenoBaseFunctional genomic aAnalysis of E. coli in Japan
GénolevuresA comparison of S. cerevisiae and 14 other yeast species
GenoListAn integrated environment for comparative analysis of microbial genomes
Genome AtlasDNA structural properties of sequenced genomes
Genome Database for RosaceaeGenetics and genomics data on apple, cherry, peach, pear, raspberry, rose and strawberry
Genome Information BrokerDDBJ’s collection of genome databases
Genome Project DBNCBI’s database of large-scale genome sequencing projects
Genome ReviewsIntegrated view of complete genomes
GenomeRNAiCell-based RNAi phenotypes database
GenomeTraFaCConserved regulatory elements of human and mouse genes
Genomic Threading DBStructural annotations of complete genomes
GénoPlante-InfoPlant genomic data from the Génoplante consortium
GenProtECE. coli K12 genome and proteome database
GENSATGene Expression Nervous System Atlas: a map of gene expression in the central nervous system of the mouse
GEOGene Expression Omnibus: Public gene expression repository
GermOnlineGene expression in mitotic and meiotic cell cycle
GISSDGroup I Intron Sequence and Structure Database
GLIDAG-protein coupled receptors ligand database
GlycanCarbohydrate database, part of the KEGG system
Glycoconjugate Data BankAnnotated structures of glycan molecules
GlycoMaps DBConformational maps of disaccharides
GlycoSuiteDBN- and O-linked glycan structures and biological sources
GOGene ontology consortium database
GOAGene Ontology Annotation
GOBASEOrganelle genome database
GOLDGenomes online database: a listing of completed and ongoing genome projects
GOLD.dbGenomics Of Lipid-associated Disorders
GOPaDGene Ontology Partition Database
GPCRDBG protein-coupled receptors database
gpDBG-protein database: G-proteins and their interaction with GPCRs
GPX-MacrophageGene expression in macrophages
GrainGenesGenes and phenotypes of wheat, barley, rye, triticale, oats
GrameneA resource for comparative grass genomics
GreengenesMultiple sequence alignment of prokaryotic 16S rDNA
GreenPhylDBComparative genomics of rice and Arabidopsis thaliana
GreglistG-quadruplex motifs and potentially G-quadruplex regulated genes
GRSDBG-rich sequences database
GTOPProtein fold predictions from genome sequences
G-tRNA-dbGenomic tRNA Database
GXDMouse Gene Expression Database
GyDBGypsy database of mobile genetic elements
HaemBFactor IX gene mutations, insertions and deletions
HAGRHuman ageing genomic resources: Genes related to ageing in humans and model organisms
HapMap ProjectA haplotype map of the human genome with patterns of DNA sequence variation
HaptendbCurated database of hapten molecules
HbVarHuman hemoglobin variants and thalassemias
HCADHuman chromosome aberration database: Chromosomal breakpoints and affected genes
HCV DatabaseHepatitis C Virus (HCV) Sequence Database
HCVdbHepatitis C Virus Database
H-DBASHuman database of alternative splicing
HDBaseA website for Huntington’s disease research
Hedgehog signallingResources and annotations of the Hedgehog signaling pathway
HEG-DBPredicted highly expressed genes in prokaryotic genomes
HemBaseGenes expressed in differentiating human erythroid cells
Heme Protein DBHeme protein structure, heme type, axial ligands, and heme protein reduction potential (Em) values
HemoPDBHematopoietic Promoter Database
HepSeqEpidemiological, clinical, and sequence data on the Hepatitis B virus hepatitis_open/main.php
HERVdHuman Endogenous Retrovirus database
Het-PDB NaviHetero-atoms in protein structures
HGMDHuman gene mutation databaseRequires user registration
HGNC DatabaseThe HUGO Gene Nomenclature Database (formerly Genew)
HGT-DBHorizontal Gene Transfer-DataBase
HGVbaseHuman genome variation database: Curated human polymorphisms
HGVS DatabasesA compilation of human mutation databases
HIC-UpHetero-compound Information Centre – Uppsala
H-InvDBFull-length human cDNA clones
Histone DatabaseHistone fold sequences and structures
HitsDatabase of protein domains and motifs
HIV Drug Resistance DatabaseHIV mutations that confer resistance to anti-HIV drugs
HIV Molecular Immunology DatabaseHIV epitopes
HIV Positive Selection Mutation DatabasePositively selected mutations in HIV-1 protease and reverse transcriptase
HIV RT and Protease Sequence DatabaseHIV reverse transcriptase and protease sequences
HIV Sequence DBHIV RNA sequences
HMDBThe Human Metabolome Database: Curated human metabolite and metabolism data
HMPDHuman mitochondrial protein database
HmtDBHuman mitochondrial database
HOINVGENHomologous invertebrate genes
HollywoodExon annotation database
Homeobox PageHomeobox proteins, classification, and evolution
Homeodomain ResourceHomeodomain sequences, structures, and related genetic and genomic information
HomoloGeneAutomatically detected homologous genes in complete eukaryotic genomes
HomophilaDrosophila homologs of human disease genes
HomophilaDrosophila homologs of human disease genes
HOMSTRADHomologous structure alignment database: curated structure-based alignments for protein families
HoppsigenHuman and mouse homologous processed pseudogenes
HORDEHuman Olfactory Receptor Data Exploratorium
HotSprintHot spots (functionally and structurally important residues) in protein interfaces
HOWDYHuman organized whole genome database
HOX-PROHomeobox genes database
hp-DPIDatabase of protein interactions in Helicobacter pylori
HPIDHuman protein interaction database
HPMRHuman plasma membrane receptome: sequences, literature, and expression data
HPRDHuman protein reference database: domain architecture, post-translational modifications, and disease association
HPTAAHuman potential tumor-associated antigens
HS3DHomo Sapiens Splice Sites Dataset
HSSPHomology-derived structures of proteins
HTPSELEXTranscription factor binding site sequences obtained using high-throughput SELEX method
HUGEHuman unidentified gene-encoded large (>50 kDa) protein and cDNA sequences
HuGEIndexHuman Gene Expression Index: Expression levels in normal tissues
Human BAC Ends DBNon-redundant human BAC end sequences
Human Genome Seg-mental Duplication DBSegmental duplications in the human genome
Human MtDBHuman mitochondrial genome database
Human p53, human hprt, rodent lacI and rodent lacZ databasesMutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
Human PAML BrowserPositive selection in human genes detected through genome comparison
Human PAX2 Allelic Variant DatabaseMutations in human PAX2 gene
Human PAX6 Allelic Variant DatabaseMutations in human PAX6 gene
HumHotHuman meiotic recombination hot spots
HuSiDaHuman siRNA database
HvrBase++Primate mitochondrial DNA control region sequences
HyPaLibHybrid pattern library: structural elements in classes of RNANot actively maintained
I2DInterologous Interaction Database: Predicted protein-protein interactions in humans
IARC TP53 DatabaseHuman TP53 somatic and germline mutations
ICBgyrB database for identification of bacteria
IDBDInfectious Disease Biomarker Database
IL2RgbaseX-linked severe combined immunodeficiency mutation database
IMB Jena Image LibraryVisualization and analysis of 3D biopolymer structures
IMGComparative analysis of microbial genomes sequenced at the DOE Joint Genome Institute
IMG/MA data management and analysis system for metagenomes
IMGTInternational immunogenetics information system: Immunoglobulins, T cell receptors, MHC, and RPI
IMGT/3Dstructure-DB3D structures of Immunoglobulins, T cell receptors, and MHC proteins
IMGT/GENE-DBVertebrate immunoglobulin and T cell receptor genes
IMGT/HLAPolymorphism of human MHC and related genes
IMGT/LIGM-DBImmunoglobulin, T cell receptor and MHC nucleotide sequences from human and other vertebrates
IMGT/PRIMER-DBImmunogenetics oligonucleotide primer database
Immune epitope DBAntibody and T cell epitopes for primates, rodents, and other animals
IMOTdbSpatially interacting motifs in proteins
Imprinted Gene CatalogueImprinted genes and parent-of-origin effects in animals
InBaseInteins (protein splicing elements) database: properties, sequences, bibliography
INEIntegrated rice genome explorer
INFEVERSHereditary inflammatory disorder and familial mediterranean fever mutation data
Influenza Virus ResourceProtein and nucleotide sequences of the influenza virus
InparanoidDatabase of eukaryotic orthologs
InSatDbSequences and properties of insect microsatellites
IntActProtein-protein interaction data
Integr8Functional classification of proteins in whole genomes
IntEnzIntegrated enzyme database and enzyme nomenclature
InterActive FlyDrosophila genes and their roles in development
Inter-Chain Beta-SheetsProtein interactions mediated by interchain beta-sheet formation
InterDomPutative protein domain interactions
InterDomPutative protein domain interactions
Interferon Stimulated Gene DatabaseGenes induced by treatment with interferons
InterFilHuman Intermediate Filament database
International Gene Trap Consortium DBPublicly available gene trap cell lines in mouse
InterProIntegrated resource of protein families, domains and functional sites
Interrupted coding sequences DBInterrupted coding sequences: frameshifts, stop codons, sequencing errors in microbial genomes
IntroneratorAlternative splicing in C. elegans and C. briggsae
IntroneratorIntrons and splicing in C. elegans and C. briggsae
IPDImmuno Polymorphism Database
IPD-ESTDABImmunologically characterised melanoma cell lines
IPD-HPAHuman platelet antigens
IPD-KIRKiller-cell Immunoglobulin-like Receptors
IPD-MHCSequences of the major histocompatibility complex
IPIInternational Protein Index
iProClassIntegrated protein classification database
iProLINKAnnotated literature sources for protein features and names
IRESdb –the Internal Ribosome Entry Site database
IRESiteExperimentally studied internal ribosome entry sites
IRIS –International Rice Information System
ISfinderInsertion sequences from bacteria and archaea
IslanderPathogenicity islands and prophages in bacterial genomes
ITS2Predicted structures of internal transcribed spacer 2 (ITS2) molecules
ITTACAIntegrated tumor transcriptome array and clinical data analysis
IUBMB Nomenclature databaseNomenclature of enzymes, membrane transporters, electron transport proteins and other proteins
IUPAC Nomenclature databaseNomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission
IUPHAR-RDInternational Union of Pharmacology recommendations on receptor nomenclature and drug classification
IVDBInfluenza Virus Database : Annotated sequences and geographic distribution of the influenza virus
IXDBPhysical maps of human chromosome X
JASPARPSSMs for transcription factor DNA-binding sites
JenPepQuantitative binding data for peptides and proteins of immunological interestSuperseded by AntiJen, no. 799
JSNPJapanese SNP database
KaryotypeDBKaryotype and chromosome data for animal and plant species
KBERGKnowledgeBase for Estrogen Responsive Genes
KDBIKinetic data of bio-molecular interactions
KEGGKyoto Encyclopedia of Genes and Genomes: databases on genes, proteins, and metabolic pathways
KEGG PathwayMetabolic and regulatory pathways in complete genomes
Kidney Development DatabaseKidney development and gene expression
KinGKinases in Genomes: Ser/Thr/Tyr kinases encoded in the completely sequenced genomes
KinMutBaseDisease-causing protein kinase mutations
KlothoCollection and categorization of biological compounds
Knottin databaseDatabase of knottins, small proteins with an unusual “disulfide through disulfide” knot
KOGEukaryotic Orthologous Groups of proteins
L1BaseFunctional annotation and prediction of LINE-1 elements
LEGERPost-genome research of Listeria
Legume Information SystemLegume information server (formerly Medicago genome initiative): ESTs, gene expression and proteomic data
LeptoListLeptospira interrogans genome
LGICdbLigand-gated ion channel subunit sequences database
LIFEdbLocalization, interaction and functions of human proteins
LIGANDChemical compounds and reactions in biological pathways
LigAsiteBiologically relevant binding sites in proteins with known structures
Lipase Engineering DBSequence, structure and function of lipases and esterases
Lipid MAPSLipid metabolites and pathways strategy
LOCATESubcellular localization of mouse proteins
LOLAList of lists annotated: a comparison of gene sets identified in different microarray experiments
Lowe Syndrome Mutation DatabaseMutations causing Lowe oculocerebrorenal syndrome
LOX-DBMammalian, invertebrate, plant and fungal lipoxygenases
LPFCLibrary of protein family core structures
LumbriBASEESTs of the earthworm Lumbricus rubellus
M3DMany Microbe Microarrays Database
MACiEMechanism, annotation and classification in enzymes: enzyme reaction mechanisms
MAGESTAscidian (Halocynthia roretzi) gene expression patterns
Magnaporthe grisea DBMagnaporthe grisea Database
MaizeGDBMaize genetics and genomics database
MALISAMManual alignments for structurally analogous motifs in proteins
MAMEPMolecular Anatomy of the Mouse Embryo Project
Mammalian Gene CollectionFull-length open reading frame clones for human, mouse, and rat genes
MamMiBaseMammalian mitochondrial genome database
MamPolMammalia Polymorphism Database
Map ViewerDisplay of genomic information by chromosomal position
MAPPERPutative transcription factor binding sites in various genomes
MAPUMax-Planck Unified proteome database
MAtDBMIPS Arabidopsis thaliana database
MBGDMicrobial genome database for comparative analysis
MedicCycBiochemical pathways in Medicago truncatula
MegaMotifbaseStructural motifs in protein families and superfamilies
MeGXMarine ecological genomix: genomics and metagenomics of marine bacteria
MEPDGene expression in medaka (freshwater fish Oryzias latipes)
MeRNAMetal ion binding sites in RNA
MEROPSDatabase of proteolytic enzymes (peptidases)
MetaCropBiochemical pathways and enzymes in crop plants
MetaCycMetabolic pathways and enzymes from various organisms
MetaCycMetabolic pathways and enzymes from various organisms
MetaGrowthGrowth requirements of bacterial pathogens
Metalloprotein Site DBMetal-binding sites in metalloproteins
MetaRouterCompounds and pathways related to bioremediation
MethDBDNA methylation data, patterns and profiles
MethyCancerLinks between DNA methylation levels and cancer
MFunGDMIPS mouse functional genomics database
MHCBNDatabase of MHC binding and non-binding peptides
MHCPEPMHC-binding peptides
MICdbProkaryotic microsatelliteshttp://
MiCroKitMidbody, Centrosome and Kinetochore proteins
microRNA.orgmicroRNA target predictions and expression profiles
MiMIMichigan Molecular Interactions: Protein-protein interactions
MINTMolecular INTeraction
MIPS resourcesMunich Information Center for Protein Sequences databases
MIPSPlantsDBMIPS Plants Databases
miRBaseMicroRNA sequences, names, and predicted targets in animals
miRGatormicroRNA target prediction, functional analysis, and gene expression data
miRGenAnimal microRNAs located in introns, exons, UTRs, pseudogenes and CpG islands
miRNAMapmicroRNA precursors and their mapping to targets in vertebrate genomes
MiSTMicrobial Signal Transduction database
MitochondriomeMetazoan mitochondrial genes
MitoDatMitochondrial proteins (predominantly human)
MitoDromeNuclear-encoded mitochondrial proteins of Drosophila
MITOMAPHuman mitochondrial genome
MitomeComparative analysis of metazoan mitochondrial genomes
MITOP2Mitochondrial proteins, genes and diseases
MitoProteomeExperimentally described human mitochondrial proteins
MitoResNuclear genes coding for mitochondrial proteins
MMDBAll experimentally-determined 3D structures, linked to NCBI Entrez
MNCDBMIPS Neurospora crassa database
Mobile group II intronsDatabase for mobile group II introns
ModBaseAnnotated comparative protein structure models
MODOMICSDatabase of RNA modification pathways
MolliGenGenomic data on mollicutes
MolMovDBDatabase of Macromolecular Movements
Monosaccharide BrowserSpace filling Fischer projections of monosaccharides
MOsDBMIPS Oryza sativa database
Mouse Genome DBFormerly mouse genome database
Mouse Phenome DBphenotypic and genotypic data from inbred strains of mice
Mouse SAGESAGE libraries from various mouse tissues and cell lines
Mouse Transposon Insertion DatabaseMouse Transposon Insertion Database
Mouse Tumor BiologyTumor types, genes, classification, incidence, pathology
MpactYeast protein-protein interaction data
MPDBMolecular Probe Database
MPIDMHC-Peptide Interaction Database
MPIMP dbMitochondrial protein import machinery of plants and yeast
MPromDBMammalian promoter database
MSY Breakpoint MapperSequence-tagged sites in the human Y chromosome
MtbRegListMycobacterium tuberculosis gene regulation
MtDBMedicago trunculata Database
MUGEN Mouse DBMurine models of immune processes and immunological diseases
MulPSSMMultiple PSSMs of structural and sequence families
MutDBPredicted biochemical effects of human genetic variation: maping of SNPs on protein sequence and structure
MvirDBProtein toxins, virulence factors, and antibiotic resistance genes
NarcisseConserved syntenies for various animal, plant and bacterial genomes
NASCarraysNottingham Arabidopsis Stock Centre microarray database
NATsDBNatural Antisense Transcripts database
NCBI Protein databaseAll protein sequences: translated from GenBank and imported from other protein databases
NCBI Taxonomy BrowserNames of all organisms that are represented in GenBank
NCBI Viral GenomesViral genome resource at NCBI
NCIRNon-Canonical Interactions in RNA
NCL ResourcePolymorphisms in neuronal ceroid lipofuscinoses genes
ncRNAs databaseNon-coding RNAs with regulatory functions
NDBNucleic acid-containing structures
NegProtNegative Proteome: A tool for comparison of complete proteomes
NEIbankEyeSAGE, EyeBrowse and Eye Disease Gene databases
Nematode.netParasitic nematode sequencing project
NEMBASENematode sequence and functional data database
NESbaseNuclear export signals database
NetAffxPublic Affymetrix probesets and annotations
NetworKINNetwork approach to human protein kinases and their substrates
NLSdbNuclear localization signals
NMPdbNuclear matrix associated proteins database
NMPDRDatabase for functional annotation and comparative analysis of microbial genomes
NONCODEDatabase of noncoding RNAs
Non-Human Genome Segmental Duplication DBSegmental duplications in mouse, dog and chicken genomes
NOPdb:Nucleolar proteome database
NORINEDatabase of nonribosomal peptides
NPDNuclear Protein Database
NPInterNoncoding RNA-protein interactions
NPRDNucleosome Positioning Region Database LibInfo+-id+2Xnp11RCiPU+-lib+NUCLEOSOME
NRESTdbNatural Rubber EST Database
NRSubNon-redundant Bacillus subtilis database at U. Lyon
NTDBThermodynamic data for nucleic acids
Nuclear Receptor ResourceNuclear receptor superfamily
NucleaRDBNuclear receptor superfamily
NUREBASENuclear hormone receptors database
NURSANuclear receptor signaling atlas
ODBOperon database
OGDOomycete Genomics Database: ESTs and annotation
O-GLYCBASEO- and C-linked glycosylation sites in proteins
OGReOrganellar Genome Resource
Olfactory Receptor DBSequences for olfactory receptor-like molecules
OMIAOnline Mendelian Inheritance in Animals
OMIMOnline Mendelian inheritance in man: A catalog of human genetic and genomic disorders
OncoDB.HCCOncogenomic database of hepatocellular carcinoma
OncoMineCancer microarray data by gene or cancer type
ooTFDObject-oriented transcription factors database
Open Proteomics DBMass-spectrometry-based proteomics data for human, yeast, E. coli and Mycobacterium
openSputnikPlant EST clustering and functional annotationNo longer maintained
OPHIDOnline predicted human interaction databaseSuperseded by I2D (no. 897)
OPTICOrthologous and Paralogous Transcripts in Clades
Oral Cancer Gene DBCellular and molecular data for genes involved in oral cancerIncorporated into TGDBs, no. 155
ORegAnnoOpen REGulatory ANNOtation database
ORENZAORphan ENZymes database
ORFanageOrphan ORFs (ORFs with no homologs) in microbial genomesNo longer maintained
ORFDBCollection of ORFs that are sold by Invitrogen
Organelle DBOrganelle proteins and subcellular structures
Organelle genomesNCBI’s organelle genome resource
OriDBDNA Replication Origin Database: Confirmed and predicted sites
OrthoDBAn hierarchical catalog of orthologous proteins in metazoa
OrthoMCLOrthologous protein clusters from multiple genomes
OryGenesDBRice genes, T-DNA and Ds flanking sequence tags
Oryza Tag LineT-DNA insertion mutants of rice
OryzabaseRice genetics and genomics
Osteo-Promoter DBGenes in osteogenic proliferation and differentiation
PACRATArchaeal and bacterial intergenic sequence featuresNo longer maintained
PA-GOSUBProtein sequences from model organisms, GO assignment and subcellular localization
PAHdbMutations at the phenylalanine hydroxylase locus
PAIDBPathogenicity islands in bacterial genomes
PairsDBPairwise alignments of all sequences in UniProt
PALIPhylogeny and alignment of homologous protein structures
PANDITProtein and associated nucleotide domains with inferred trees
PANTHERProtein sequence evolution mapped to functions and pathways
PanzeaMaize genome project data
ParaDBParalogy mapping in human genomes
ParameciumDBParamecium genome sequencing project
PartiGeneDBAssembled partial genomes for ~250 eukaryotic organisms
PASS2Structural motifs of protein superfamilies
PathBaseEuropean mutant mice histopathology database: images
PathDBBiochemical pathways, compounds and metabolismNo longer maintained
PathguideA listing of pathway, signal transduction and protein-protein interaction databases
PathoPlantSignal transduction related to plant-pathogen interactions
PatomeAnnotated sequences from patents and patent applications
PATRICPathoSystems Resource Integration Center
PBmicepiggyBac transposon insertions in the mouse genome.
PDBProtein Data Bank: all known protein structures
PDB_TMTransmembrane proteins with known 3D structure
PDB-Ligand3D structures of small molecules bound to proteins and nucleic acids
PDB-REPRDBRepresentative protein chains, based on PDB entries
PDBSite3D structure of protein functional sites
PDBsumSummaries and analyses of PDB structures
PDZBaseProtein-protein interactions involving PDZ domains
PECProfiling of E. coli Chromosome
PEDANTResults of an automated analysis of genomic sequences
PEDEPig Expression Data Explorer: Pig cDNA libraries and ESTs
PEPPredictions for Entire Proteomes
PepConfDBDatabase of peptide conformations
PepCyber:P~PepHuman protein interactions mediated by phosphoprotein-binding domains
PEPRPublic Expression Profiling Resource
PepSeekerPeptide identification and ion information from proteome experiments
PeptaibolPeptaibol (antibiotic peptide) sequences
PeptideAtlasPeptides identified in LC-MS/MS proteomics experiments
PeroxisomeDBPeroxisomal proteins, metabolic routes and diagnostic tools
PfamProtein families: Multiple sequence alignments and profile hidden Markov models of protein domains
PFDProtein Folding Database : Experimental data on protein folding
PGDBProstate and prostatic diseases gene database
PGTdbProkaryotic growth temperature database
PGTdbProkaryotic growth temperature database
PharmGEDPharmacoGenetic Effect Database
PharmGKBPharmacogenomics and Pharmacogenetics Knowledge Base
PhenomicDBComparison of phenotypes of orthologous genes in human and model organisms
PHEXdbPHEX mutations causing X-linked hypophosphatemia
PHI-baseGenes affecting fungal pathogen-host interactions
PhosPhAtArabidopsis Protein Phosphorylation Site Database
Phospho.ELMS/T/Y protein phosphorylation sites (former PhosphoBase)
Phospho3D3D structures of protein phosphorylation sites
PhyloFactsPhylogenomic analysis of protein families
PhylomeDBExperimentally validated and predicted serine phosphorylation sites in Arabidopsis thaliana
PhytomeComparative genomics of plant species
Phytophthora Functional Genomics DBESTs and expression data from P. infestans and P. sojae
PhytoProtClusters of (predicted) plant proteins
PIDDProtein inter-atomic distances database
PigGISPig genome mapping, genes and ESTs
PINdbProteins interacting in nucleus (human and yeast)
PINTProtein-protein interactions thermodynamic database
PIRProtein Information Resource
piRNABankSequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat
PIRSFFamily/superfamily classification of whole proteins
PLACEPlant cis-acting regulatory DNA elements
Plant DNA C-values DatabaseGenome sizes of various plants and algae
Plant Genome CentralNCBI’s portal for various large-scale plant genome and EST sequencing projects
Plant MPSSMassively parallel signature sequencing of plant genes
Plant Ontology DBControlled vocabulary of plant structures and growth stages
Plant Organelles DBImages and protocols for plant organelle research
Plant snoRNA DBsnoRNA genes in plant species
Plant Stress-Responsive Gene CatalogStress-responsive gene in various plant species
PlantCAREPlant promoters and cis-acting regulatory elements
PlantGDBPlant genome database: Actively-transcribed plant genes
PlantMarkersDatabase of predicted molecular markers from plants
PLANT-PIsPlant protease inhibitors
PlantPromPlant promoter sequences for RNA polymerase II
PlantQTL-GEQuantitative trait locus analysis in Arabidopsis and rice
PlantsP/PlantsTPlant proteins involved in phosphorylation and transport
PlantTFDBPlant Transcription Factor Database
PlantTribesFamilies of protein-coding genes from five sequenced plant species
PlasmIDA repository for collection and distribution of plasmid clones
PlasmoDBPlasmodium genome database
PLMItRNAMitochondrial tRNA genes in photosynthetic eukaryotes
PLPMDBPyridoxal-5′-phosphate dependent enzymes mutations
PLprotPlastid protein database
PMDB3D protein models obtained from structure predictions
POGs/PlantRBPOrthologous groups of RNA binding proteins in plants
POINTPrediction of human protein-protein interactome
PolyA_DBDatabase of mammalian mRNA polyadenylation
PolyDomsHuman coding SNPs mapped onto protein domains
PolymiRTSPolymorphism in microRNA Target Site
PolymorphixDatabase of sequence polymorphisms
PoMaMoPotato Maps and More
Poxvirus.orgPoxvirus genomic sequences and gene annotation
PPDExperimentally-determined protein pKa values
PPDBPlant promoter database
PPNEMAPlant-parasitic nematode rRNAs
PPT-DBProtein Property Prediction and Testing Database
PRECISEPredicted and Consensus Interaction Sites in Enzymes
PReModPredicted transcriptional regulatory modules in the human genome
PRFProtein research foundation database of peptides
PRIDEProteomics peptide identification database
Primer StudioPCR primers for eukaryotic and prokaryotic genes
PRINTSHierarchical gene family fingerprints
Pristionchus.orgGenome data of the nematode Pristionchus pacificus
probeBaserRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated information
PROCOGNATEProtein cognate ligands for the domains in enzyme structures
ProDomProtein domain families
PRODORICProkaryotic database of gene regulation networks
ProLysEDDatabase of bacterial protease systems
ProlysisProteases and natural and synthetic protease inhibitors
PromECE. coli promoters with experimentally-identified transcriptional start sites
PROMISEProsthetic centers and metal ions in protein active sites
ProNITProtein-nucleic acid interactions
PROPHECYProfiling of phenotypic characteristics in yeast
ProRuleFunctional and structural information on PROSITE profiles
ProSASProtein Structure and Alternative Splicing: effects of alternative splicing events on protein structure
PROSITEBiologically-significant protein patterns and profiles
Prostate Expression DBProstate expression database: ESTs from prostate tissue and cell type-specific cDNA libraries
PROTCOM3D structures of two-chain protein complexes
Protein kinase resourceProtein kinase resource: sequences, enzymology, genetics and molecular and structural properties
Protein Mutant DBCompilation of protein mutant data
ProTeusSignature sequences at the protein N- and C-termini
ProThermThermodynamic data for wild-type and mutant proteins
ProTISATranslation Initiation Site Annotation in prokaryotic genomes
ProtoMapHierarchical classification of Swiss-Prot proteins
ProtoNetHierarchical clustering of Swiss-Prot proteins
ProtozoaDBComparative analysis of protozoan genomes
PRRDBPattern recognition receptors and their ligands
PRTADProtein residue torsion angle database
PseudoBaseDatabase of RNA pseudoknots
PseudoCAPPseudomonas aeruginosa community genome annotation project
PseudoGene.orgPseudogenes in eukaryotic and prokaryotic genomes
PSIbaseInteraction of proteins with known 3D structures
PSORTdbProtein subcellular localization in bacteria
pSTIINGProtein signalling, transcriptional interactions and inflammation networks gateway
PTCH1 Mutation DBMutations and SNPs found in PTCH1 gene
PubChemStructures and biological activities of small organic molecules
PubMedCitations and abstracts of biomedical literature
PubMethLinks between DNA methylation levels and cancer
PUMA2Metabolic analysis of complete microbial genomes
QPPDQuantitative PCR Primer Database
qPrimerDepotQuantitative real time PCR primers for human RefSeq sequences
QTL MatchmakerQuantitative trait loci mapping in human, mouse and rat
QuadBaseG-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes
R.E.DD.B.RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments
RAP-DBRice annotation project database
RARGERIKEN Arabidopsis genome encyclopedia: cDNAs, mutants and microarray data
Rat Genome DatabaseRat genetic and genomic data
RatMapRat genome tools and data
RB1 Gene Mutation DBMutations in the human retinoblastoma (RB1) gene
RDP-IIRibosomal Database Project
ReactomeDatabase of metabolic and signaling pathways
REBASERestriction enzymes and associated methylases
RECODEGenes using programmed translational recoding in their expression
REDflyRegulatory modules and transcription factor binding sites in Drosophila
REDIdbAn RNA editing database
RefExAReference database for human gene expression analysis
REFOLDExperimental data on protein refolding and purification
RefSeqReference Sequence database: an integrated, non-redundant set of genomic DNA, RNA, and protein sequences
RegTransBaseManually curated database of regulatory interactions in prokaryotes
RegulonDBTranscriptional regulation and operon organization in E.coli
RESIDPost-translational modifications of proteins
RetrOryzaLTR-retrotransposons in rice
RfamNon-coding RNA families
RHdbRadiation hybrid map data
Rice Annotation DBContig data for manual annotation of rice genome
Rice Mutant DatabaseRice mutant database
Rice PipelineUnification tool for rice databases
Rice Proteome DBRice proteome database
RiceGAASRice genome automated annotation system
RIDOMRibosomal Differentiation of Medical Microorganisms
RISSCRibosomal Internal Spacer Sequence Collection
RNA FRABASEDatabase of 3D RNA fragments within known RNA structures
RNA Modification DBNaturally modified nucleosides in RNA
RNA SSTRANDRNA secondary structure data and structural motifs
RNABaseRNA-containing structures from PDB and NDB
RNAdbMammalian noncoding RNA database
RNAi codexClones from mouse, human and rat shRNA libraries
RNAiDBRNAi phenotypic analysis of C. elegans genes
RNAJunctionRNA structural elements: helical junctions, internal loops, bulges and loop-loop interactions
RNAse P DatabaseRibonuclease P sequences, alignments and structures
RNRdbRibonucleotide reductase database
rOGEDRat ovarian gene expression database
ROSPathReactive oxygen species (ROS) signaling pathway
RoundupRepository of orthologs and corresponding evolutionary distances
RPGRibosomal Protein Gene database
RRNDBrRNA operon numbers in various prokaryotes
RsGDBRhodobacter sphaeroides genome
rSNP GuideSNPs in regulatory gene regions
RTCGDRetroviral Tagged Cancer Gene Database
RTKdbReceptor Tyrosine Kinase database
RTPrimerDBReal-time PCR primer and probe sequences
S/MARt DBNuclear scaffold/matrix attached regions
S4Structure-based Sequence Alignments of SCOP Superfamilies
SAGEmapNCBI’s resource for SAGE data from various organisms
SARS-CoV RNA SSSPredicted secondary structures of SARS coronavirus RNA
SBASEProtein domain sequences and tools
SCAdbSpinocerebellar ataxia candidate gene database
SCMDSaccharomyces cerevisiae morphological database: micrographs of budding yeast mutants
SCOPStructural classification of proteins
SCOPECMapping of catalytic function to domain structure
SCOPPIStructural classification of protein-protein interfaces
SCORStructural classification of RNA: RNA motifs by structure, function and tertiary interactions
ScorpionDatabase of scorpion toxins
SCPDSaccharomyces cerevisiae promoter database
SCPDSaccharomyces cerevisiae promoter database
SDAPStructural database of allergenic proteins and food allergens
SebidaSex bias in insect gene expression database
Secreted Protein DBSecreted proteins from human, mouse and rat
SeedGenesGenes essential for Arabidopsis development
SelenoDBDatabase of selenoprotein genes, proteins and SECIS elements
SELEXdbSelected DNA/RNA functional site sequences
SENTRASensory signal transduction proteins
SEVENS7-transmembrane helix receptors (G-protein-coupled)
SGCEdbStructural genomics of C. elegansNo longer maintained
SGDSaccharomyces genome database
SGMDSoybean genomics and microarray database
Shanghai Rapeseed DatabaseSeed development and fatty acid metabolism of oilseed crops
ShiBaseShigella database
SIDDBaseStress-induced DNA duplex destabilization profiles of complete microbial genomes
SIEGESmoking Induced Epithelial Gene Expression
SilkDBSilkworm Bombyx mori ESTs, mutants, photographs
SilkSatDbA microsatellite database of the silkworm Bombyx morihttp://
SIMAPSimilarity matrix of proteins: precomputed similarity data
siRecordsExperimentally tested mammalian siRNAs
siRNAdbFunctional human siRNA sequences
SISYPHUSStructural alignments for proteins with non-trivial relationships
SitesBaseKnown ligand binding sites in the PDB
SKY/M-FISH and CGHFluorescent images of chromosomes and cytogenetic data
SLoopClassification of protein loops
Small RNA DatabaseNo longer maintained 
SMARTSimple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains
SmedGDThe Schmidtea mediterranea genome database
SNAPAn integrated SNP Annotation Platform
SNAPPIStructures, iNterfaces and Alignments for Protein-Protein Interactions
Sno/scaRNAbaseSmall nucleolar RNAs and cajal body-specific RNAs
snoRNA-LBME-dbHuman snoRNAs and Cajal body-specific RNAs (scaRNAs)
[email protected]Human SNPs and genes that contain human ethnic variation
SNP2NMDHuman SNPs causing nonsense-mediated mRNA decay
SNP500CancerRe-sequenced SNPs from 102 reference samples
SNPeffect & PupaSuitePhenotypic effects of human coding SNPs
SNPSTRMicrosatellite compound markers in 5 vertebrate genomes
SOURCEFunctional genomics resource for human, mouse and rat
SoyBaseGenetic, genomic and phenotypic information about soybean
SoyGDSoybean genome database
SPEEDSearchable prototype experimental evolutionary database
SpliceDBCanonical and non-canonical mammalian splice sites
SpliceInfoModes of alternative splicing in human genome
SpliceNestVisualizing Splicing of Genes from EST Data
SpodoBaseGenomics of the butterfly Spodoptera frugiperda
SRPDBSignal recognition particle database
SSToSSSequence-Structural Templates of Single-member Superfamilies
STACKSequence tag alignment and consensus knowledgebase
Stanford Microarray DBRaw and normalized data from microarray experiments
STCDBSignal Transduction Classification Database
StellaBaseNematostella vectensis (sea anemone) genome
STING ReportAmino acid properties in proteins of known structure
STITCHSearch Tool for Interactions of Chemicals
STRBaseShort tandem DNA repeats database
STRINGPredicted functional associations between proteins
Structurally conserved interfacesInteracting residues in protein-protein interfaces in PDB
Structure Superposition DatabasePairwise superpositions of 115 TIM-barrel structures
SUBASubcellular localisation of Arabidopsis proteins
SubtiListBacillus subtilis genome database at Institut Pasteur
Subviral RNA DBDatabase of viroids and viroid-like RNAs
Sulfolobus DatabaseComparative genomics of Sulfolobus species
SuperCATDatabase for multilocus sequence typing analysis of the Bacillus cereus group of bacteria
SuperDrug2D and 3D chemical structures of various drugs
SUPERFAMILYAssignments of proteins to structural superfamilies
SuperHaptenA comprehensive database for small immunogenic compounds
SuperNaturalNatural compounds and their suppliers
SuperTargetDrug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins
SUPFAMGrouping of sequence families into superfamilies
SURFACESurface residues and functions annotated, compared and evaluated: a database of protein surface patches
SV40 Large T-Antigen Mutant DatabaseMutations in SV40 large tumor antigen gene
SWEET-DBAnnotated carbohydrate structure and substance information
SWISS-2DPAGEAnnotated 2D gel electrophoresis database
SWISS-MODEL Repository3D protein structure models generated by automated homology modeling using SWISS-MODEL
SwissRegulon databaseGenome-wide annotations of regulatory sites in the intergenic regions
SynDBSynapse protein database
Synthetic Gene DBSynthetic genes described in peer-reviewed literature
SYSTERSSystematic re-searching and clustering of proteins
SYSTOMONASSYSTems biology of pseudOMONAS
T1DbaseA resource for type 1 diabetes research
T4-like genome DBSequences of T4-like bacteriophages from various sources
TAEDThe Adaptive Evolution Database: plant and chordate gene families
TAIRThe Arabidopsis information resource
TargetDBTarget data from worldwide structural genomics projects
TassDBTAndem Splice Site Database
TBestDBTaxonomically broad EST database: protist ESTs
TCDBTransporter protein classification database
TcruziDBTrypanosoma cruzi genome database
TECRdbThermodynamics of enzyme-catalyzed reactions
TEDTomato expression database
Telomerase databaseSequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components
TESSTranscription element search system
Tetrahymena Genome DBTetrahymena thermophila genome database
The Autism Chromoso-me Rearrangement DBCurated collection of genomic features related to autism
The Cell Cycle DBGenes and proteins involved in human and yeast cell cycle
The Chromosome 7 Annotation ProjectHuman chromosome 7 sequence and annotation
The Lafora DatabaseThe Lafora progressive myoclonus epilepsy mutation and polymorphism database
The Small Subunit rRNA Modification DBModified nucleosides in small subunit rRNA
THGSTransmembrane Helices in Genome Sequences
TIGR Comprehensive Microbial ResourceVarious data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteins
TIGR Gene IndicesOrganism-specific databases of EST and gene sequences
TIGR Maize databaseMaize genome sequencing consortium site
TIGR Microbial DBA list of microbial genome sequencing projectsNo longer maintained
TIGR plant repeat DBClassification of repetitive sequences in plant genomes
TIGR Plant Transcript Assembly databaseTranscript assemblies of plant EST and cDNA sequences
TIGRFAMsTIGR protein families adapted for functional annotation
TiProDTissue-specific promoter database
TMADThe Stanford Tissue Microarray Database
TmaDBTissue microarray database
TMBETA-GENOMEBeta-barrel membrane proteins encoded in various genomes
tmRDBtmRNA database
tmRNA WebsitetmRNA sequences and alignments
TomatEST DBEST collection from multiple tomato species
TopDBTopology Data Bank of transmembrane proteins
TOPOFIT-DBProtein structural alignments based on the TOPOFIT method
TopoSNPTopographic database of non-synonymous SNPs
TOPSTopology Of Protein Structures
ToxoDBToxoplasma gondii genome database
TPMDTaiwan polymorphic microsatellite marker database
Tractor_DBTranscription factors in gamma-proteobacteria database
TRANSCompel®Transcriptional regulation, composite regulatory elements databases.html#transcompel
TRANSFAC®Transcription factors, gene regulation, positional weight matrices
TransfactomeDBNucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors
Transmembrane Protein DatabaseTransmembrane proteins with experimentally-characterized transmembrane topologies
TRANSPATHSignal transduction pathways, vizualization and expression data analysis
TranspoGeneTransposed elements influence on the transcriptome of seven vertebrates and invertebrates
TransportDBPredicted membrane transporters in complete genomes, classified according to the TC classification system
TranstermCodon usage, start and stop signals
TRBaseTandem repeats in the human genome
TRDBTandem repeats in genomic DNA
TREDTranscriptional regulatory element database
Tree of LifeInformation on phylogeny and biodiversity
TreeBasePhylogenetic trees and the data matrices used to generate them
TreeFamTree families database: phylogenetic trees of animal genes
T-REGsA list of TGFbeta-responsive genesNo longer maintained
TRIPLESTransposon-insertion phenotypes, localization, and expression in Saccharomyces
tRNA SequencesHas not been updated 
trome, trEST, trGENDatabases of predicted human protein sequences
TropGENE DBGenes and genomes of sugarcane, banana, cocoa
TRRDTranscription regulatory regions of eukaryotic genes
TrSDBTranscription factor database
TTDTherapeutic target database
Tumor Gene Family Databases (TGDBs)Cellular, molecular and biological data about genes involved in various cancers
Tumor-Associated Genes DatabaseTumor-associated genes database
U12DBDatabase of orthologous U12-type spliceosomal introns
UCSC Archaeal Genome BrowserPyrococcus furiosus genome browser
UCSC Genome BrowserGenome assemblies and annotation
UCSD-Nature Signaling GatewayExpert-authored and peer-reviewed information on mammalian proteins involved in cellular signaling
U-genomeGenome organization in unicellular eukaryotes
UgMicroSatdbUniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes
UK CropNetGenome mapping in crop plants
UM-BBDUniversity of Minnesota biocatalysis and biodegradation database
UMLSUnified medical language systemRequires user registration
UniGeneUnified clusters of ESTs and full-length mRNA sequences
UniHIUnified Human Interactome: human protein-protein interactions
UniParcUniProt archive, a repository of all protein sequences
UniProtUniversal Protein knowledgebase, combined information from Swiss-Prot, TrEMBL, and PIR
UniProtKB\Swiss-ProtFormerly SwissProt, part of the UniProt knowledgebase
UniProtKB\TrEMBLNow UniProt/TrEMBL, part of the UniProt knowledgebase
UniRefClustered sets of related sequences from UniProt
UniSaveUniProtKB Sequence/Annotation Version Archive
UniSTSUnified view of sequence tagged sites with mapping data
UniTrapUnambiguous insertions in the same subgenic regions of annotated mouse genes
UniVecVector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contamination
University of Pittsburgh Bioinformatics Resources CollectionA collection of bioinformatic databases and software tools
UTGB/medakaUniversity of Tokyo Genome Browser of medaka fish (Oryzias latipes) genomic data
UTRdb/UTRsite5′- and 3′-UTRs of eukaryotic mRNAs
UTRome3’UTRs and their functional elements in C. elegans
VBASE2Variable genes from the Ig loci of human and mouse
VBI Microbial DatabaseVirginia Bioinformatics Institute microbial database
VectorBaseInvertebrate Vectors of Human Pathogens
VectordbCharacterization and classification of nucleic acid vectors
VEGAVertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences
VFDBVirulence Factors of pathogenic bacteria
VIDAHomologous viral protein families database
VIOLINVaccine Investigation and Online Information Network
VIPERdbVirus particle explorer: Virus capsid structures
Viral Bioinformatics Resource CenterVirus orthologous genes, gene families and genomes
VirGenCurated database for complete viral genome sequences
Vir-Mir dbPrediction of viral microRNA candidate hairpins
VirOligoVirus-specific oligonucleotides for PCR and hybridization
VISTA Enhancer BrowserEnhancer elements in the human genome
ViTamicroRNAs targets of the influenza virus
VKCDBVoltage-gated K+ Channel Database
VNTR Locus DBBacterial Variable Number Tandem Repeat locus database
WAtDBWageningen Arabidopsis thaliana DatabaseNo longer maintained
wFleaBaseDaphnia Water Flea Genome Database
Wnt DatabaseWnt proteins and phenotypes
WorfDBC. elegans ORFeome
WormBaseData repository for C. elegans and C. briggsae: curated genome annotation, genetic and physical maps, pathways
WormBookPeer-reviewed chapters on the biology of C. elegans
X:MAPAnnotation and visualization of genome structure for Affymetrix exon array analysis
xanthusBaseGenome of the social bacterium Myxococcus xanthus
xBaseA family of group-specific bacterial genome databases, includes coliBASE, CampyDB, ClostriDB, MycoDB, PseudoDB and others
XenBaseXenopus genomics resource
XproEukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes
YDPMYeast deletion project and mitochondria database
Yeast Intron DatabaseAres lab database of splicesomal introns in S. cerevisiae
Yeast Intron DatabaseAres lab database of splicesomal introns in S. cerevisiae introns.html
Yeast snoRNA DatabaseYeast small nucleolar RNAs
Yeast snoRNA DBYeast small nucleolar RNAs Yeast_snoRNA_Database/snoRNA_DataBase.html
YEASTRACTYeast transcriptional regulation
YEASTRACTYeast search for transcriptional regulators and consensus tracking
YGOBYeast gene order browser
yMGVYeast microarray global viewer
YMPDYeast mitochondrial protein database
YRC PDRYeast resource center public data repository
ZFINZebrafish information network