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All Databases : Biotechnology,Biochemistry,Molecular Biology , Bioinformatics, Neuroinformatics, cheminformatics, immunoinformatics,Pharmainformatics,Genomics and proteomics

Database of genome , proteome , Bioinformatics from various laboratories and institution
Database and LinksDescription
DDBJDNA Data Bank of Japan All known nucleotide and protein sequences
EMBLNucleotide Sequence Database All known nucleotide and protein sequences
GenBank1All known nucleotide and protein sequences
ACLAME Aclassification of genetic mobile elements
CUTGCodon usage tabulated from GenBank
Genetic CodesGenetic codes in various organisms and organelles
Entrez GeneGene-centered information at NCBI
HERVd Human endogenous retrovirus database
HoppsigenHuman and mouse homologous processed pseudogenes
Imprinted Gene CatalogueImprinted genes and parent-of-origin effects in animals
IslanderPathogenicity islands and prophages in bacterial genomes
MICdbProkaryotic microsatellites
NPRDNucleosome positioning region database
STRBaseShort tandem DNA repeats database
TIGRGene Indices Organism-specific databases of EST and gene sequences
TranstermCodon usage, start and stop signals
UniGeneNon-redundant set of eukaryotic gene-oriented clusters
UniVecVector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
VectorDBCharacterization and classification of nucleic acid vectors
XproEukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes
ASAPAlternative spliced isoforms
ASDAlternative splicing database at EBI, includes three databases AltSplice,AltExtron and Aedb
ASDBAlternative splicing database: protein products and expression patternsof alternatively spliced genes
ASHESdbAlternatively spliced human genes by exon skipping database
EASEDExtended alternatively spliced EST database
ECgeneGenome annotation for alternative splicing
EDASEST-derived alternative splicing database
ExIntExon–intron structure of eukaryotic genes
HS3DHomo sapiens splice sites dataset
IntroneratorAlternative splicing in C.elegans and C.briggsae
SpliceDBCanonical and non-canonical mammalian splice sites
SpliceInfoModes of alternative splicing in human genome
SpliceNestA tool for visualizing splicing of genes from EST data
ACTIVITYFunctional DNA/RNA site activity
DBTBSBacillus subtilis promoters and transcription factors
DoOPDatabase of orthologous promoters: chordates and plants
DPInteractBinding sites for E.coli DNA-binding proteins
HemoPDBHematopoietic promoter database: transcriptional regulation in hematopoiesis
JASPARPSSMs for transcription factor DNA-binding sites
MAPPERPutative transcription factor binding sites in various genomes
PLACEPlant cis-acting regulatory DNA elements
PlantCAREPlant promoters and cis-acting regulatory elements
PlantPromPlant promoter sequences for RNA polymerase II
PromECE.coli promoters with experimentally identified transcriptional start sites
SELEX_DBDNA and RNA binding sites for various proteins, found by systematicevolution of ligands by exponential enrichment
TESSTranscription element search system
TRACTOR dbTranscription factors in gamma-proteobacteria database
TRANSCompelComposite regulatory elements affecting gene transcription in eukaryotes
TRANSFACTranscription factors and binding sites
TREDTranscriptional regulatory element database
TRRDTranscription regulatory regions of eukaryotic genes
16S and 23S rRNA Mutation Database16S and 23S ribosomal RNA mutations
5S rRNA Database5S rRNA sequences
Aptamer databaseSmall RNA/DNA molecules binding nucleic acids, proteins
AREDAU-rich element-containing mRNA database
Mobile group II intronsA database of group II introns, self-splicing catalytic RNAs
European rRNA databaseAll complete or nearly complete rRNA sequences
GtRDBGenomic tRNA database
Guide RNA DatabaseRNA editing in various kinetoplastid species
HIV Sequence DatabaseHIV RNA sequences
HuSiDaHuman siRNA database
HyPaLibHybrid pattern library: structural elements in classes of RNA
IRESdbInternal ribosome entry site database
microRNARegistry Database of microRNAs (small non-coding RNAs)
NCIRNon-canonical interactions in RNA structures
ncRNAs DatabaseNon-coding RNAs with regulatory functions
NONCODEA database of non-coding RNAs
PLANTncRNAsPlant non-coding RNAs
Plant snoRNA DBsnoRNA genes in plant species
PolyA_DBA database of mammalian mRNA polyadenylation
PseudoBaseDatabase of RNA pseudoknots
RfamNon-coding RNA families
RISSCRibosomal internal spacer sequence collection
RNAdbMammalian non-coding RNA database
RNA Modification DatabaseNaturally modified nucleosides in RNA
RRNDBrRNA operon numbers in various prokaryotes
siRNAdbsiRNA database and search engine
Small RNA DatabaseSmall RNAs from prokaryotes and eukaryotes
SRPDBSignal recognition particle database
SSU rRNA Modification DatabaseModified nucleosides in small subunit rRNA
SubviralRNA Database Viroids and viroid-like RNAs
tmRNAtmRNA sequences and alignments
tmRDBtmRNA database
tRNAsequences tRNA viewer and sequence editor
UTRdb50- and 30-UTRs of eukaryotic mRNAs
EXProtSequences of proteins with experimentally verified function
NCBIProtein database All protein sequences: translated from GenBank and imported from other protein databases
PA-GOSUBProtein sequences from model organisms, GO assignment and subcellular localization
PIR-PSDProtein information resource protein sequence database, has been merged into the UniProt knowledgebase
PIR-NREFPIR’s non-redundant reference protein database
PRFProtein research foundation database of peptides: sequences, literature and unnatural amino acids
Swiss-ProtSwiss-Prot Now UniProt/Swiss-Prot: expertly curated protein sequence database,section of the UniProt knowledgebase
TrEMBLNow UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase
UniParcUniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence
UniProtUniversal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databases
UniRefUniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms)
AAindexPhysicochemical properties of amino acids
ProNITThermodynamic data on protein–nucleic acid interactions
ProThermThermodynamic data for wild-type and mutant proteins
TECRdbThermodynamics of enzyme-catalyzed reactions
DBSubLocDatabase of protein subcellular localization
NESbaseNuclear export signals database
NLSdbNuclear localization signals
NMPdb Nuclear matrix associated proteins database
NOPdb Nucleolar proteome database
PSORTdbProtein subcellular localization in bacteria
SPD Secreted protein database
THGSTransmembrane helices in genome sequences
TMPDBExperimentally characterized transmembrane topologies
ASCActive sequence collection: biologically active peptides
BlocksAlignments of conserved regions in protein families
CSACSA Catalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure
COMeCo-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins)
CopSComprehensive peptide signature database
eBLOCKSHighly conserved protein sequence blocks
eMOTIFProtein sequence motif determination and searches
Metalloprotein Site DatabaseMetal-binding sites in metalloproteins
O-GlycBaseO- and C-linked glycosylation sites in proteins
PDBSite3D structure of protein functional sites
PhosphoELM S/T/Y protein phosphorylation sites (formerly PhosphoBase)
PROMISEProsthetic centers and metal ions in protein active sites
PROSITEBiologically significant protein patterns and profiles
ProTeusSignature sequences at the protein N- and C-termini
ADDAA database of protein domain classification
CDDConserved domain database, includes protein domains fromPfam, SMART, COG and KOG databases
CluSTrClusters of Swiss-Prot+TrEMBL proteins
FunShiftFunctional divergence between the subfamilies of a protein domain family
HitsA database of protein domains and motifs
InterProIntegrated resource of protein families, domains and functional sites
iProClassIntegrated protein classification database
PIRSFFamily/superfamily classification of whole proteins
PRINTSHierarchical gene family fingerprints
PfamProtein families: multiple sequence alignments and profile hidden Markov models of protein domains
PRECISEPredicted and consensus interaction sites in enzymes
ProDomProtein domain families
ProtoMapHierarchical classification of Swiss-Prot proteins
ProtoNetHierarchical clustering of Swiss-Prot proteins
S4Structure-based sequence alignments of SCOP superfamilies
SBASEProtein domain sequences and tools
SMARTSimple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains
SUPFAMGrouping of sequence families into superfamilies
SYSTERSSystematic re-searching and clustering of proteins
TIGRFAMsTIGR protein families adapted for functional annotation
AARSDBAminoacyl-tRNA synthetase database
ASPDArtificial selected proteins/peptides database
BacTregulatorsTranscriptional regulators of AraC and TetR families
CSDBaseCold shock domain-containing proteins
CuticleDBStructural proteins of Arthropod cuticle
DCCPDatabase of copper-chelating proteins
DExH /D Family Database DEAD-box, DEAH-box and DExH-box proteins
Endogenous GPCR List G protein-coupled receptors; expression in cell lines
ESTHEREsterases and other alpha/beta hydrolase enzymes
EyeSite Families of proteins functioning in the eye
GPCRDB G protein-coupled receptors database
gpDBG-proteins and their interaction with GPCRs
Histone Database Histone fold sequences and structures
Homeobox Homeobox pageHomeobox proteins, classification and evolution
Hox-ProHomeobox genes database
Homeodomain Resource Homeodomain sequences, structures and related genetic and genomic information
HORDEHuman olfactory receptor data exploratorium
InBaseInteins (protein splicing elements) database: properties, sequences, bibliography
KinGKinases in Genomes S/T/Y-specific protein kinases encoded in complete genomes
KnottinsDatabase of knottins—small proteins with an unusual ‘disulfide through disulfide’ knot
LGICdbLigand-gated ion channel subunit sequences database
Lipase Engineering DatabaseLipase Engineering Database Sequence, structure and function of lipases and esterases
LOX-DBMammalian, invertebrate, plant and fungal lipoxygenases
MEROPSDatabase of proteolytic enzymes (peptidases)
NPDNuclear protein database
NucleaRDBNuclear receptor superfamily
NRRNuclear Receptor Resource Nuclear receptor superfamily
NUREBASENuclear hormone receptors database
Olfactory Receptor DatabaseSequences for olfactory receptor-like molecules
ooTFDObject-oriented transcription factors database
PKRProtein kinase resource: sequences, enzymology, genetics and molecular and structural properties
PLPMDBPyridoxal-50-phosphate dependent enzymes mutations
ProLysEDA database of bacterial protease systems
ProlysisProteases and natural and synthetic protease inhibitors
REBASERestriction enzymes and associated methylases
Ribonuclease P DatabaseRibonuclease P Database
RPGRibosomal protein gene database
RTKdb Receptor tyrosine kinase sequences
S/MARt dBNuclear scaffold/matrix attached regions
ScorpionDatabase of scorpion toxins
SDAPStructural database of allergenic proteins and food allergens
SENTRA Sensory signal transduction proteins
SEVENS 7transmembrane helix receptors (G-protein-coupled)
SRPDBProteins of the signal recognition particles
TrSDBTranscription factor database
VKCDBVoltage-gated potassium channel database
Wnt DatabaseWnt proteins and phenotypes
ChEBIChemical entities of biological interest
CSD Cambridge structural database: crystal structure information for organic and metal-organic compounds
UppsalaHIC-Up Hetero-compound Information Centre
AANTAmino acid–nucleotide interaction database
KlothoCollection and categorization of biological compounds
LIGANDChemical compounds and reactions in biological pathways
PDB-Ligand3D structures of small molecules bound to proteins and nucleic acids
PubChemStructures and biological activities of small organic molecules
CCSDComplex carbohydrate structure database (CarbBank)
CSSCarbohydrate structure suite: carbohydrate 3D structures derived from the PDB
GlycanCarbohydrate database, part of the KEGG system
GlycoSuiteDB N- and O-linked glycan structures and biological sources
Monosaccharide BrowserSpace-filling Fischer projections of monosaccharides
SWEET-DBAnnotated carbohydrate structure and substance information
NDBNucleic acid-containing structures
NTDBThermodynamic data for nucleic acids
RNABaseRNA-containing structures from PDB and NDB
SCORStructural classification of RNA: RNA motifs by structure, function and tertiary interactions
ArchDBAutomated classification of protein loop structures
ASTRALSequences of domains of known structure, selected subsets and sequence– structure correspondences
BAliBASEA database for comparison of multiple sequence alignments
BioMagResBankNMR spectroscopic data for proteins and nucleic acids
CADBConformational angles in proteins database
CATHProtein domain structures database
CE 3D protein structure alignments
CKAAPsStructurally similar proteins with dissimilar sequences
DaliProtein fold classification using the Dali search engine
Decoys ‘R’ UsComputer-generated protein conformations
DisProtDatabase of Protein Disorder: proteins that lack fixed 3D structure in their native states
DomInsDomain insertions in known protein structures
DSDBASENative and modeled disulfide bonds in proteins
DSMMDatabase of simulated molecular motions
eF-siteElectrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites
GenDiSGenomic distribution of protein structural superfamilies
Gene3DPrecalculated structural assignments for whole genomes
GTD Genomic threading database: structural annotations of complete proteomes
GTOPProtein fold predictions from genome sequences
HetPDB Navi Hetero-atoms in protein structures
HOMSTRADHomologous structure alignment database: curated structure-based alignments for protein families
IMB JenaImage Library Visualization and analysis of 3D biopolymer structures
IMGT/3Dstructure DBSequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins
ISSDIntegrated sequence–structure database
LPFCLibrary of protein family core structures
MMDBNCBI’s database of 3D structures, part of NCBI Entrez
E-MSD EBI’s macromolecular structure database
ModBaseAnnotated comparative protein structure models
MolMovDBDatabase of macromolecular movements: descriptions of protein and macromolecular motions, including movies
PALIPhylogeny and alignment of homologous protein structures
PASS2Structural motifs of protein superfamilies
PepConfDBA database of peptide conformations
PDBProtein structure databank: all publicly available 3D structures of proteins and nucleic acids
PDB-REPRDBRepresentative protein chains, based on PDB entries
PDBsumSummaries and analyses of PDB structures
PDB_TMTransmembrane proteins with known 3D structure
Protein Folding DatabaseExperimental data on protein folding
SCOPStructural classification of proteins
SloopClassification of protein loops
Structure Superposition DatabasePairwise superposition of TIM-barrel structures
SWISS-MODELRepository Database of annotated 3D protein structure models
SUPERFAMILYAssignments of proteins to structural superfamilies
SURFACESurface residues and functions annotated, compared and evaluated: a database of protein surface patches
TargetDBTarget data from worldwide structural genomics projects
3D-GENOMICSStructural annotations for complete proteomes
TOPSTopology of protein structures database
GenewHuman gene nomenclature: approved gene symbols
GOGene ontology consortium database
GOAEBI’s gene ontology annotation project
IUBMBNomenclature database Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins
IUPACNomenclature database Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission
IUPHAR-RDThe International Union of Pharmacology recommendations on receptor nomenclature and drug classification
PANTHERGene products organized by biological function
UMLSUnified medical language system
ICB gyrBdatabase for identification and classification of bacteria
NCBI TaxonomyNames of all organisms represented in GenBank
PANDITProtein and associated nucleotide domains with inferred trees
RIDOMrRNA-based differentiation of medical microorganisms
RDP-IIRibosomal database project
PhylogenyTree of Life Information on phylogeny and biodiversity
COGClusters of orthologous groups of proteins
COGENTComplete genome tracking: predicted peptides from fully sequenced genomes
CORGComparative regulatory genomics: conserved non-coding sequence blocks
DEGDatabase of essential genes from bacteria and yeast
EBI GenomesEBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
EGOEukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices
EMGlibEnhanced microbial genomes library: completely sequenced genomes of unicellular organisms
Entrez GenomesNCBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
ERGOLightIntegrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database
FusionDBDatabase of bacterial and archaeal gene fusion events
Genome AtlasDNA structural properties of sequenced genomes
Genome Information BrokerDDBJ’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes
Genome ReviewsIntegrated view of complete genomes
GOLDGenomes online database: a listing of completed and ongoing genome projects
HGT-DBPutative horizontally transferred genes in prokaryotic genomes
Integr8Functional classification of proteins in whole genomes
KEGGKyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins and metabolic pathways
MBGDMicrobial genome database for comparative analysis
ORFanageDatabase of orphan ORFs (ORFs with no homologs) in complete microbial genomes
PACRATArchaeal and bacterial intergenic sequence features
PartiGeneDBAssembled partial genomes for _250 eukaryotic organisms
PEDANTResults of an automated analysis of genomic sequences
TIGR ComprehensiveMicrobial Resource Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins
TransportDBPredicted membrane transporters in complete genomes, classified according to the TC classification system
WIT3What is there? Metabolic reconstruction for completely sequenced microbial genomes
HCVDBThe hepatitis C virus database
HIV Drug Resistance DatabaseHIV mutations that confer resistance to anti-HIV drugs
HIV Molecular Immunology DatabaseHIV Molecular Immunology Database HIV epitopes
HIV RT and Protease Sequence DatabaseHIV RT and Protease Sequence Database HIV reverse transcriptase and protease sequences
NCBI Viral GenomesNCBI Viral Genomes Viral genome resource at NCBI
PoxvirusPoxvirus genomic sequences and gene annotation
T4-like genome databaseSequences of T4-like bacteriophages from various sources
VIDAHomologous viral protein families database
VIPERVirus particle explorer: virus capsid structures
VirOligoVirus-specific oligonucleotides for PCR and hybridization
BacMapPicture atlas of annotated bacterial genomes
MetaGrowthGrowth requirements of bacterial pathogens
PGTdbProkaryotic growth temperature database
CyberCell databaseA collection of data on E.coli K12 intended for mathematical modeling to simulate the bacterial cell
coliBaseA database for E.coli, Salmonella and Shigella
ColibriE.coli genome database at Institut Pasteur
EchoBASEPost-genomic studies of Escherichia coli
GenoBaseGenoBase E.coli genome database at Nara Institute
GenProtECE.coli K12 genome and proteome database
PECProfiling of E.coli chromosome
EcoCycE.coli K12 genes, metabolic pathways, transporters and gene regulation
EcoGeneSequence and literature data on E.coli genes and proteins
RegulonDBTranscriptional regulation and operon organization in E.coli
BSORFBacillus subtilis genome database at Kyoto U
NRSubNon-redundant Bacillus subtilis database at U. Lyon
SubtiListBacillus subtilis genome database at Institut Pasteur
BioCycPathway/genome databases for many bacteria
CampyDBDatabase for Campylobacter genome analysis
ClostriDBFinished and unfinished genomes of Clostridium spp
CIDBChlamydia Interactive Database: gene expression data
CyanoBaseCyanobacterial genomes
LeptoListLeptospira interrogans genome
MolliGenGenomic data on mollicutes
PseudoCAPPseudomonas aeruginosa genome database and community annotation project
RsGDBRhodobacter sphaeroides genome
VirFactBacterial virulence factors and pathogenicity islands
Factors Reference database for microbial virulence factors
ApiEST-DBEST sequences from various Apicomplexan parasites
CryptoDBCryptosporidium parvum genome database
Diatom EST DatabaseESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum
DictyBaseUniversal resource for Dictyostelium discoideum
Full-MalariaFull-length cDNA library from erythrocytic-stage Plasmodium falciparum
GeneDBCurated database for various Sanger-sequenced genomes
LumbriBASEESTs of the earthworm Lumbricus rubellus
PlasmoDBPlasmodium genome database
TcruziDBTrypanosoma cruzi genome database
ToxoDBToxoplasma gondii genome database
AGDAshbya gossypii genome database
CandidaDBCandida albicans genome database
Candida GenomeCandida albicans genome database
CYGD MIPSComprehensive yeast genome database
GenolevuresA comparison of S.cerevisiae and 14 other yeast species
PROPHECYProfiling of phenotypic characteristics in yeast
SCMDSaccharomyces cerevisiae morphological database: micrographs of budding yeast mutants
SCPDSaccharomyces cerevisiae promoter database
SGDSaccharomyces genome database
TRIPLESTransposon-insertion phenotypes, localization and expression in Saccharomyces
YDPMYeast deletion project and mitochondria database
Yeast Intron DatabaseAres lab database of splicesomal introns in S.cerevisiae
snoRNA DatabaseYeast small nucleolar RNAs
yMGVYeast microarray global viewer
YRC PDRYeast resource center public data repository
CADRECentral Aspergillus data repository
COGEME Phytopathogenic fungi and oomycete EST database
MNCDBMIPS Neurospora crassa database
OGDOomycete Genomics Database: ESTs and annotation
PhytophthoraFunctional Genomics Database ESTs and expression data from P.infestans and P.sojae
IntroneratorIntrons and splicing in C.elegans and C.briggsae
RNAiDBRNAi phenotypic analysis of C.elegans genes
WILMAC.elegans annotation database
WorfDBC.elegans ORFeome
WormBaseData repository for C.elegans and C.briggsae: curated genome annotation, genetic and physical maps, pathways
FlyBaseDrosophila sequences and genomic information
FlyBrainDatabase of the Drosophila nervous system
FlyMineIntegration of insect genomic and proteomic data
FlyTrapDrosophila mutants created using GFP protein trap strategy
GadFlyGenome annotation database of Drosophila
GeniSysEnhancer- and promoter-inserted mutants of Drosophila
DPDBDrosophila polymorphism database
Drosophilamicroarray project Data and tools for Drosophila gene expression studies
InterActiveFly Drosophila genes and their roles in development
AppaDBA database on the nematode Pristionchus pacificus
BeetleBaseGenome database of the beetle Tribolium castaneum
CiliateIES-MDS Db Macro- and micronuclear genes in spirotrichous ciliates
CnidBaseCnidarian evolution and gene expression database
NematodeParasitic nematode sequencing project
NEMBASENematode sequence and functional data database
PPNEMAPlant-parasitic nematode rRNAs
SilkDBSilkworm Bombyx mori ESTs, mutants, photographs
SilkSatDbA microsatellite database of the silkworm Bombyx mori
SpodoBaseGenomics of the butterfly Spodoptera frugiperda
BRENDAEnzyme names and biochemical properties
ENZYME Enzyme nomenclature and properties
EzCatDBEnzyme Catalytic Mechanism Database
IntEnzIntegrated enzyme database and enzyme nomenclature
PDBrtfRepresentation of target families of enzymes in PDB
SCOPECMapping of catalytic function to domain structure
BioSilicoIntegrated access to various metabolic databases
MetaCycMetabolic pathways and enzymes from various organisms
PathDBBiochemical pathways, compounds and metabolism
UM-BBDUniversity of Minnesota biocatalysis and biodegradation database
3DID3D interacting domains: domain–domain interactions in proteins with known 3D structures
aMAZEA system for the annotation, management, and analysis of biochemical and signalling pathway networks
BINDBiomolecular interaction network database
BioCartaOnline maps of metabolic and signaling pathways
BRITEBiomolecular relations in information transmission and expression, part of KEGG
DDIBDatabase of domain interactions and binding
DIPDatabase of interacting proteins: experimentally determined protein–protein interactions
DRCDatabase of ribosomal crosslinks
GeneNetDatabase on gene network components
hp-DPIDatabase of protein interactions in Helicobacter pylori
HPIDHuman protein interaction database
IntActproject Protein–protein interaction data
Inter-ChainBeta-Sheets Protein–protein interactions mediated by interchain beta-sheet formation
InterDomPutative protein domain interactions
PDZBaseProtein–protein interactions involving PDZ domains
Proteinprotein interfaces Interacting residues in protein–protein interfaces in PDB
PINdbProteins interacting in nucleus (human and yeast)
POINTPrediction of human protein–protein interactome
PSIbaseInteraction of proteins with known 3D structures
ReactomeA knowledgebase of biological pathways
ROSPath Reactive oxygen species (ROS) signaling pathway
STCDBSignal transductions classification database
STRINGPredicted functional associations between proteins
TRANSPATHGene regulatory networks and microarray analysis
ACeDBC.elegans, S.pombe and human genomic information
AllGenesHuman and mouse gene, transcript and protein annotation
ArkDBGenome databases for farm and other animals
ChickVDSequence variation in the chicken genome
CreTransgenic Database Cre transgenic mouse lines with links to publications
DEDDatabase of evolutionary distances
EnsemblAnnotated information on eukaryotic genomes
FANTOMFunctional annotation of mouse full-length cDNA clones
FREPFunctional repeats in mouse cDNAs
GALAGenomic alignment, annotation and experimental results
GenetPigGenes controlling economic traits in pig
HomoloGeneAutomatically detected homologous genes in complete eukaryotic genomes
InparanoidA database of eukaryotic orthologs
IPIInternational protein index: non-redundant sets of human, mouse and rat proteins
KaryotypeDBKaryotype and chromosome information for animal and plant species
KOGEukaryotic orthologous groups of proteins
Mouse Genome InformaticsMouse Genome Informatics Formerly mouse genome database
MTIDMouse transposon insertion database
NegProtNegative Proteome: a tool for comparison of complete proteomes
PEDEPig EST data explorer: full-length cDNAs and ESTs
PhenomicDBComparison of phenotypes of orthologous genes in human and model organisms
PolymorphixA database of sequence polymorphisms
Rat Genome Database Rat Genome Database Rat genetic and genomic data
RatMapRat genome tools and data
TAEDThe adaptive evolution database: a phylogeny-based tool for comparative genomics
TIGRGene Indices Organism-specific databases of EST and gene sequences
UniGeneUnified clusters of ESTs and full-length mRNA sequences
UniSTSUnified view of sequence tagged sites with mapping data
VEGAVertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences
ZFINZebrafish information network
EnsemblAnnotated information on eukaryotic genomes
AluGeneComplete Alu map in the human genome
CroW 21Human chromosome 21 database
GB4-RHGenebridge4 human radiation hybrid maps
GDBHuman genes and genomic maps
GenAtlasHuman genes, markers and phenotypes
GeneCardsIntegrated database of human genes, maps, proteins and diseases
GeneLocGene location database (formerly UDB—Unified database for human genome mapping)
GeneNestGene indices of human, mouse, zebrafish, etc
GenMapDBMapped human BAC clones
GRLGene Resource Locator Alignment of ESTs with finished human sequence
HOWDY Human organized whole genome database
HuGeMapHuman genome genetic and physical map data
HumGenHuman BAC Ends Non-redundant human BAC end sequences
HumanDupHuman Genome Segmental Duplication Database Segmental duplications in the human genome
IXDBPhysical maps of human chromosome X
L1BaseFunctional annotation and prediction of LINE-1 elements
Map ViewerMap Viewer Display of genomic information by chromosomal position
MGCMammalian genome collection: full-length ORFs for human, mouse and rat genes
NCBI RefSeqNon-redundant collection of naturally occurring biological molecules
ParaDBParalogy mapping in human genomes
RHdbRadiation hybrid map data
SKYSKY/M-FISH and CGH Fluorescent images of chromosomes and cytogenetic data
STACKSequence tag alignment and consensus knowledgebase
The Chromosome 7The Chromosome 7 Annotation Project A comprehensive description of human chromosome 7
TRBaseTandem repeats in the human genome
UCSCGenome Browser Genome assemblies and annotation
H-InvDBFull-length human cDNA clones
HPMRHuman plasma membrane receptome: sequences, literature and expression data
HPRDHuman protein reference database: domain architecture, post-translational modifications and disease association
HUNTHuman novel transcripts: annotated full-length cDNAs
HUGEHuman unidentified gene-encoded large (>50 kDa) protein and cDNA sequences
LIFEdbLocalization, interaction and functions of human proteins
trOme, trEST and trGENDatabases of predicted human protein sequences
HCADHuman chromosome aberration database: chromosomal breakpoints and affected genes
OMIAOnline Mendelian inheritance in animals: a catalog of animal genetic and genomic disorders
OMIMOnline Mendelian inheritance in man: a catalog of human genetic and genomic disorders
ORFDBCollection of ORFs that are sold by Invitrogen
PathBaseEuropean mutant mice histopathology database: images
PMDCompilation of protein mutant data
SOURCEFunctional genomics resource for human, mouse and rat
ALFREDAllele frequencies and DNA polymorphisms
BayGenomicsGenes relevant to cardiovascular and pulmonary disease
Cypriotnational mutation database Disease mutations in the Cypriot population
Database of Genomic VariantsHuman genomic variants: frequency, segmental duplications and genome assembly gaps
dbQSNPQuantification of SNP allele frequencies database
dbSNPDatabase of single nucleotide polymorphisms
Functional element SNPs database: SNPs located within promoters, UTRs, etc., of human genes
HGVSDatabases A compilation of human mutation databases
HGVbaseHuman genome variation database: curated human polymorphisms
HGMDHuman gene mutation database
IPDImmuno polymorphism database
JSNPJapanese SNP database
rSNPGuide SNPs in regulatory gene regions
SNP Consortium database SNP Consortium data
SNPeffectPhenotypic effects of human coding SNPs
TopoSNPTopographic database of non-synonymous SNPs
TPMDTaiwan polymorphic microsatellite marker database
Cancer AtlasAtlas of Genetics and Cytogenetics in Oncology and Haematology Cancer-related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseases
CancerChromosomesCancer Chromosomes Cytogenetic, clinical and reference information on cancer-related aberrations
CGED Cancer gene expression database
COSMIC Catalogue of somatic mutations in cancer: sequence data, samples and publications
GermlineGermline p53 Mutations Mutations in human tumor and cell line p53 gene
IARCTP53 Database Human TP53 somatic and germline mutations
MTBMouse tumor biology database: tumor types, genes, classification, incidence, pathology
OncoMineCancer microarray data by gene or cancer type
Oral Cancer Gene DatabaseCellular and molecular data for genes involved in oral cancer
RB1 Gene Mutation DBMutations in the human retinoblastoma (RB1) gene
RTCGDRTCGD Mouse retroviral tagged cancer gene database
SNP500SNP500Cancer Re-sequenced SNPs from 102 reference samples
SV40Large T-Antigen Mutants Mutations in SV40 large tumor antigen gene
Tumor Gene Family DatabasesCellular, molecular and biological data about genes involved in various cancers
ALPSbaseAutoimmune lymphoproliferative syndrome database
AndrogenAndrogen Receptor Gene Mutations Database Mutations in the androgen receptor gene
BTKbaseMutation registry for X-linked agammaglobulinemia
CarpeDBComprehensive database on the genetics of epilepsy
CASRDBCalcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidism
cytokine4Cytokine Gene Polymorphism in Human Disease Cytokine gene polymorphism literature database
Collagen Mutation Database Human type I and type III collagen gene mutations
ERGDBEstrogen responsive genes database
FUNPEPLow-complexity peptides capable of forming amyloid plaque
GOLDGenomics of lipid-associated disorders database
GRAPMutants of G-protein coupled receptors of family A
HaemBFactor IX gene mutations, insertions and deletions
HbVarHuman hemoglobin variants and thalassemias
HAGRHuman ageing genomic resources: genes related to ageing in humans and model organisms
Human p53Human p53/hprt, rodent lacI/lacZ databases Mutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
Human PAX2Allelic Variant Database Mutations in human PAX2 gene
Human PAX6Allelic Variant Database Mutations in human PAX6 gene
INFEVERSHereditary inflammatory disorder and familial mediterranean fever mutation data
KinMutBaseDisease-causing protein kinase mutations
LoweSyndrome Mutation Database Mutations causing Lowe oculocerebrorenal syndrome
NCLMutation Database Polymorphisms in neuronal ceroid lipofuscinoses genes
PAHdbMutations at the phenylalanine hydroxylase locus
PGDBProstate and prostatic diseases gene database
PHEXdbPHEX mutations causing X-linked hypophosphatemia
PTCH1Mutation Database Mutations and SNPs found in PTCH1 gene
SCAdbSpinocerebellar ataxia candidate gene database
T1DbaseA resource for type 1 diabetes research
AutismThe Autism Chromosome Rearrangement Database Curated collection of genomic features related to autism
LaforaThe Lafora Database Mutations and polymorphisms associated with Lafora progressive myoclonus epilepsy
50SAGE50-end serial analysis of gene expression
ArrayExpressPublic collection of microarray gene expression data
AxeldbGene expression in Xenopus laevis
BodyMapHuman and mouse gene expression data
BGEDBrain gene expression database
CleanExExpression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons
dbERGEIIDatabase of experimental results on gene expression: genomic alignment, annotation and experimental data
EICO DBExpression-based imprint candidate organiser: a database for discovery of novel imprinted genes
emap AtlasEdinburgh mouse atlas: a digital atlas of mouse embryo development and spatially mapped gene expression
EPConDBEndocrine pancreas consortium database
EpoDBGenes expressed during human erythropoiesis
FlyView Drosophila development and genetics
GeneAnnotRevised annotation of Affymetrix human gene probe sets
GeneNote Human genes expression profiles in healthy tissues
GenePaintGene expression patterns in the mouse
GeneTideA transcriptome-focused member of the GeneCards suite
GeneTrapExpression patterns in an embryonic stem library of gene trap insertions
GEOGene expression omnibus: gene expression profiles
GermOnlineGene expression in mitotic and meiotic cell cycle
GXDMouse gene expression database
H-ANGELHuman anatomic gene expression library
HemBaseGenes expressed in differentiating human erythroid cells
HugeIndexExpression levels of human genes in normal tissues
Kidney Development DatabaseKidney development and gene expression
LOLAList of lists annotated: a comparison of gene sets identified in different microarray experiments
MAGESTAscidian (Halocynthia roretzi) gene expression patterns
MAMEPMolecular anatomy of the mouse embryo project: gene expression data on mouse embryos
MEPDMedaka (freshwater fish Oryzias latipes) gene expression pattern database
MethDBDNA methylation data, patterns and profiles
Mouse SAGESAGE libraries from various mouse tissues and cell lines
NASCarraysNottingham Arabidopsis Stock Centre microarray database
NetAffxPublic Affymetrix probesets and annotations
Osteo-Promoter DatabaseOsteo-Promoter Database Genes in osteogenic proliferation and differentiation
PEDBProstate expression database: ESTs from prostate tissue and cell typespecific cDNA libraries
PEPRPublic expression profiling resource: expression profiles in a variety of diseases and conditions
RECODEGenes using programmed translational recoding in their expression
RefExAReference database for human gene expression analysis
rOGEDRat ovarian gene expression database
SAGEmapNCBI’s resource for SAGE data from various organisms
SIEGESmoking Induced Epithelial Gene Expression
Stanford Microarray DatabaseStanford Microarray Database Raw and normalized data from microarray experiments
Tooth Development DatabaseTooth Development Database Gene expression in dental tissue
2D-PAGEProteome database system for microbial research
DynaProt2D Proteome database of Lactococcus lactis
GelBank2D gel electrophoresis patterns of proteins from complete microbial genomes
Open Proteomics DatabaseOpen Proteomics Database Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium
PEPPredictions for entire proteomes: summarized analyses of protein sequences
RESIDPre-, co- and post-translational protein modifications
SWISSSWISS-2DPAGE Annotated 2D gel electrophoresis database
ANTIMICDatabase of natural antimicrobial peptides
AOBaseAntisense oligonucleotide selection and design
APDAntimicrobial peptide database
BSDBiodegradative strain database: microorganisms that can degrade aromatic and other organic compounds
DARTDrug adverse reaction target database
MetaRouterCompounds and pathways related to bioremediation
PeptaibolPeptaibol (antibiotic peptide) sequences
PharmGKBPharmacogenomics knowledge base: effect of genetic variation on drug responses
TTDTherapeutic target database
IMGT/PRIMER-DBImmunogenetics oligonucleotide primer database
MPDB Synthetic oligonucleotides useful as primers or probes
PrimerPCRPCR primers for eukaryotic and prokaryotic genes
probeBaserRNA-targeted oligonucleotide probe sequences, DNA microarray layouts and associated information
QPPDQuantitative PCR Primer Database for human and mouse
RTPrimerDBReal-time PCR primer and probe sequences
PubMedCitations and abstracts of biomedical literature
BioImageDatabase of multidimensional biological images
GOBASEOrganelle genome database
OGReOrganelle genome retrieval system
Organelle genomesOrganelle genomes NCBI’s organelle genome resource
PLprotArabidopsis thaliana chloroplast protein database
Organelle DB Organelle proteins and subcellular structures
AMPDBArabidopsis mitochondrial protein database
HMPDHuman mitochondrial protein database
HvrBasePrimate mitochondrial DNA control region sequences
MitochondriomeMitochondriome Metazoan mitochondrial genes
MitoDatMitochondrial proteins (predominantly human)
MitoDromeNuclear-encoded mitochondrial proteins of Drosophila
MitoMapHuman mitochondrial genome
MitoNucNuclear genes coding for mitochondrial proteins
MITOP2Mitochondrial proteins, genes and diseases
MitoPDYeast mitochondrial protein database
MitoProteomeExperimentally described human mitochondrial proteins
MPIMPMitochondrial protein import machinery of plants
PLMItRNAPlant mitochondrial tRNA
BarleyBaseExpression profiling of plant genomes
CR-ESTrop ESTs: barley, pea, wheat and potato
CropNetGenome mapping in crop plants
FLAGdbIntegrative database about plant genomes
GenoPlanteInfo Plant genomic data from the Genoplante consortium
GrainGenesGenes and phenotypes of wheat, barley, rye, triticale, oats
GrameneA resource for comparative grass genomics
MendelMendel Annotated plant ESTs and STSs
openSputnikPlant EST clustering and functional annotation
PhytoProtClusters of (predicted) plant proteins
PlantMarkersA database of predicted molecular markers from plants
PlantGDBPlant genome database: actively transcribed plant genes
PLANT-PIsPlant protease inhibitors
PlantsP/PlantsTPlant proteins involved in phosphorylation and transport
TIGRplant repeat database Classification of repetitive sequences in plant genomes
TropGENE DBGenes and genomes of sugarcane, banana, cocoa
AGNSArabidopsis GeneNet supplementary: gene expression and phenotypes of mutants and transgens
AGRISArabidopsis gene regulatory information server: promoters, transcription factors and their target genes
ArabidopsisMPSS Arabidopsis gene expression detected by massively parallel signature sequencing
Arabidopsis Nucleolar Protein DatabaseArabidopsis Nucleolar Protein Database Comparative analysis of human and Arabidopsis nucleolar proteomes
ASRPArabidopsis thaliana small RNA project
ARAMEMNONArabidopsis thaliana membrane proteins and transporters
AthaMapGenome-wide map of putative transcription factor binding sites in Arabidopsis thaliana
CATMAComplete Arabidopsis transcriptome microarray
DATFDatabase of Arabidopsis transcription factors
GabiPDCentral database of the German Plant Genome Project
GeneFarmExpert annotation of Arabidopsis gene and protein families
MAtDBMIPS Arabidopsis thaliana database
RARGE RIKENArabidopsis genome encyclopedia: cDNAs, mutants and microarray data
SeedGenesGenes essential for Arabidopsis development
TAIRThe Arabidopsis information resource
WAtDBWageningen Arabidopsis thaliana database: mutants, transgenic lines and natural variants
BGI RISeBeijing genomics institute rice information system
INEIntegrated rice genome explorer
IRISInternational rice information system
MOsDBMIPS Oryza sativa database
OryzabaseRice genetics and genomics
Oryza Tag Line databaseT-DNA insertion mutants of rice
RADRice annotation database
RiceGAASRice genome automated annotation system
Rice PIPELINEUnification tool for rice databases
RiceRice proteome database Rice proteome database
database for Brassica genomic research
MaizeGDBMaize genetics and genomics database
LIS (formerly MGI)Legume information server (formerly Medicago genome initiative): ESTs, gene expression and proteomic data
MtDB Medicago trunculata genome database
PoMaMoPotato Maps and More: Potato genome data
SGMDSoybean genomics and microarray database
BCIpepA database of B-cell epitopes
dbMHCGenetic and clinical database of the human MHC
FIMM Functional molecular immunology data
HaptendbCurated database of hapten molecules
HLA Ligand/Motif A databaseHLA Ligand/Motif A database and search tool for HLA sequences
IL2RgbaseX-linked severe combined immunodeficiency mutations
IMGTInternational immunogenetics information system: immunoglobulins, T cell receptors, MHC and RPI
IMGT/Gene-DBDB Vertebrate 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
Interferon Stimulated Gene DatabaseGenes induced by treatment with interferons
IPD-ESTDABImmunologically characterized melanoma cell lines
IPD-HPAImmuno polymorphism of human platelet antigens
IPD-KIRImmuno polymorphism of killer-cell Ig-like receptors
Sequences of the major histocompatibility complex
JenPepQuantitative binding data for immunological protein–peptide interactions
MHCBNA database of MHC binding and non-binding peptides
MHCPEPMHC-binding peptides
MPID MHCpeptide interaction database
VBASE2Variable genes from the Ig loci of human and mouse
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