Abbreviations of Genetic Databases

These abbreviations are used in PubMed and refer to Molecular Biology databses.

PCR, qPCR and RT-PCR sequences and primers needed to be alligned through different databses. Today most is done by BLAST on NCBI.

Lieven Gevaert, Bio-ir, RUG 1969

Director Gentaur Database

16S and 23S rRNA Mutation Database16S and 23S ribosomal RNA mutations
16S rRNA databaseMultiple sequence alignment of prokaryotic 16S rDNA
2D-PAGEProteome database system for microbial research
3D-GENOMICSStructural annotations for complete proteomes
3DID3D interacting domains: Domain-domain interactions in proteins with known 3D structures
5S rRNA Database5S rRNA sequences
5’SAGE5′-end serial analysis of gene expression
AAindexPhysicochemical properties of amino acids
AANTAmino acid-nucleotide interaction database
AARSDBAminoacyl-tRNA synthetase 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
ADDAA database of protein domain classification
AffinDBAffinity data for protein-ligand complexes
AGDAshbya gossypii genome database
ALFREDAllele frequencies and DNA polymorphisms
AllGenesHuman and mouse gene, transcript and protein annotation
ALPSbaseAutoimmune lymphoproliferative syndrome database
AluGeneComplete Alu map in the human genome
AlzGeneCandidate genes for Alzheimer disease
Androgen Receptor Gene Mutations DatabaseMutations in the androgen receptor gene
ANTIMICDatabase of natural antimicrobial peptides
AOBaseAntisense oligonucleotide selection and design
APDAntimicrobial peptide database
ApiEST-DBEST sequences from various Apicomplexan parasites
AppaDBA database on the nematode Pristionchus pacificus
Aptamer databaseSmall RNA/DNA molecules binding nucleic acids, proteins
ArchDBAutomated classification of protein loop structures
AREDAU-rich element-containing mRNA database
ArgonauteGene regulation by mammalian microRNAs
ArkDBGenome databases for farm and other animals
ArrayExpressPublic collection of microarray gene expression data
ASAPAlternative spliced isoforms
ASAPA systematic annotation package for community analysis of E. coli and related genomes
ASCActive sequence collection: biologically-active peptides
ASDAlternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb
ASDBAlternative splicing database: protein products and expression patterns of alternatively-spliced genes
ASHESdbAlternatively spliced human genes by exon skipping
ASPDArtificial selected proteins/peptides database
ASTRALSequences of domains of known structure, selected subsets and sequence-structure correspondences
ATDAlternate transcript diversity database
Atlas of Genetics and Cytogenetics in Oncology and HaematologyCancer related genes, chromosomal abnormalities in oncology and haematology, and cancer-prone diseases
AxeldbGene expression in Xenopus laevis
BacMapPicture atlas of annotated bacterial genomes
BacTregulatorsTranscriptional regulators of AraC and TetR families
BAliBASEA database for comparison of multiple sequence alignments
BayGenomicsGenes relevant to cardiovascular and pulmonary disease
BeetleBaseGenome database of the beetle Tribolium castaneum
BGEDBrain gene expression database
BioCycPathway/genome databases for many bacteria
BioImageDatabase of multidimensional biological images
BioMagResBankNMR spectroscopic data for proteins and nucleic acids
BioModelsPublished mathematical models of biological interest
BioSilicoIntegrated access to various metabolic databases
BIOZONA database of gene and protein familiy classification
BlocksAlignments of conserved regions in protein families
BodyMapHuman and mouse gene expression data
BodyMap-XsA database for cross-species comparison of vertebrate gene expression
BRENDAEnzyme names and biochemical properties
BSDBiodegradative strain database: Microorganisms that can degrade aromatic and other organic compounds
BSORFBacillus subtilis genome database at Kyoto U.
BTKbaseMutation registry for X-linked agammaglobulinemia
C. elegans ProjectGenome sequencing data at the Sanger Institute
CADBConformational angles in proteins database
CADRECentral Aspergillus data repository
CAGECAGE tags for cap-analysis of gene expression
CampyDBDatabase for Campylobacter genome analysis
Cancer ChromosomesCytogenetic, clinical, and reference information on cancer-related aberrations
Candida GenomeCandida albicans genome database
CandidaDBCandida albicans genome database
CarpeDBComprehensive database on the genetics of epilepsy
CASRDBCalcium-sensing receptor database: CASR mutations causing hypercalcemia and/or hyperparathyroidism
CATHProtein domain structures database
CCDSConsensus CDS: collaborative effort to identify a core set of human protein coding regions
CCSDComplex carbohydrate structure database (CarbBank )
CDDConserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases
CE3D protein structure alignments
CGEDCancer gene expression database
ChEBIChemical entities of biological interest
ChickVDSequence variation in the chicken genome
ChimerDBPutative chimeric sequences in the GenBank
CIDBChlamydia Interactive Database: Gene expression data
Ciliate IES-MDS DbMacro- and micronuclear genes in spirotrichous ciliates
CisRedHuman regulatory DNA sequence motifs
CKAAPs DBStructurally-similar proteins with dissimilar sequences
CleanExExpression reference database, linking heterogeneous expression data to facilitate cross-dataset comparisons
ClostriDBFinished and unfinished genomes of Clostridium spp.
CluSTrClusters of Swiss-Prot+TrEMBL proteins
CnidBaseCnidarian evolution and gene expression database
CoCConservation of conservation: Universally conserved residues in selected protein folds
COGClusters of orthologous groups of proteins
COGEMEPhytopathogenic fungi and oomycete EST database
CoGenT++Complete genome tracking: Predicted peptides from fully sequenced genomes
coliBaseA database for E. coli, Salmonella and Shigella
ColibriE. coli genome database at Institut Pasteur
Collagen Mutation DatabaseHuman type I and type III collagen gene mutations
ColumbaAnnotation of protein structures from the PDB
COMeCo-ordination of metals etc.: classification of metalloproteins
Comparative GenometricsNucleotide frequencies and the GC and TA skews in complete genome sequences
CopSComprehensive peptide signature databasehttp://
CORGComparative regulatory genomics: conserved non-coding sequence blocks
COSMICCatalogue of somatic mutations in cancer: Sequence data, samples and publications
Cre Transgenic DatabaseCre transgenic mouse lines with links to publications
CroW 21Human chromosome 21 database
CryptoDBCryptosporidium parvum genome database
CSACatalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure
CSDCambridge structural database: Crystal structure information for organic and metal-organic compounds
CSDBaseCold shock domain-containing proteins
CSSCarbohydrate structure suite: carbohydrate 3D structures
CTGAThe catalogue for transmission genetics in Arabs
CUTGCodon usage tabulated from GenBank
CuticleDBStructural proteins of Arthropod cuticle
CyanoBaseCyanobacterial genomes
CybaseProteins with cyclic backbones
CyberCell databaseA collection of data on E. coli K12 intended for mathematical modeling to simulate the bacterial cell
CYGDMIPS Comprehensive yeast genome database
Cypriot national mutation databaseDisease mutations in the Cypriot population
Cytokine Gene Polymorphism in Human DiseaseCytokine gene polymorphism literature database
DaliProtein fold classification using the Dali search engine
DARTDrug adverse reaction target database
Database nameFull name and/or descriptionURL
Database of Genomic VariantsHuman genomic variants: frequency, segmental duplications and genome assembly gaps
DBDTranscription factor prediction database
dbERGEIIDatabase of experimental results on gene expression: Genomic alignment, annotation and experimental data
dbPTMInformation on post-translational modification of proteins
dbQSNPQuantification of SNP allele frequencies database
dbRIPHuman retrotransposon insertion polymorphism
dbSNPDatabase of single nucleotide polymorphisms
DBSubLocDatabase of protein subcellular localization
DBTBSBacillus subtilis promoters and transcription factors
DBTGRA database of tunicate (Ciona) gene regulation
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
DEDDatabase of evolutionary distances
DEGDatabase of essential genes from bacteria and yeast
DenizBeta-thalassemia allele frequencies in world populations
DExH/D Family DatabaseDEAD-box, DEAH-box and DExH-box proteins
DG-CSTDisease gene conserved sequence tagshttp://
Diatom EST DatabaseESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum
DictyBaseUniversal resource for Dictyostelium discoideum
DIPDatabase of interacting proteins: Experimentally-determined protein-protein interactions
DisProtDatabase of Protein Disorder: proteins that lack fixed 3D structure in their native states
DMAPSA database of multiple alignments for protein structures
DomInsDomain insertions in known protein structures
DoOPDatabase of orthologous promoters: chordates and plants
DPDBDrosophila polymorphism database
DPInteractBinding sites for E. coli DNA-binding proteins
DPVwebDescriptions of plant viruses
DRCDatabase of ribosomal crosslinks
Drosophila microarray projectData and tools for Drosophila gene expression studies
DrugBankCombined information on drugs and drug targets
DSDBASENative and modeled disulfide bonds in proteins
DSMMDatabase 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, metabolic pathways, transporters, and gene regulation
EcoGeneSequence and literature data on E. coli genes and proteins
EDASEST-derived alternative splicing database
eF-siteElectrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites
EGOEukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices
EHCOEncyclopedia of hepatocellular carcinoma genes online
EICO DBExpression-based imprint candidate organiser: a database for discovery of novel imprinted genes
EIDExon-intron database
EMAGEEdinburgh mouse atlas gene expression database
emap AtlasEdinburgh mouse atlas: a digital atlas of mouse embryo development and spatially-mapped gene expression
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’s macromolecular structure database
Endogenous GPCR ListG protein-coupled receptors; expression in cell lines
EnsemblAnnotated information on eukaryotic genomes
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
EPConDBEndocrine pancreas consortium database
EPDEukaryotic promoter database
EpoDBGenes expressed during human erythropoiesis
ERGDBEstrogen responsive genes database
ERGOLightIntegrated biochemical data on 9 bacterial genomes: Publicly-available portion of the ERGO database
EROP-MoscowEndogenous regulatory oligopeptide database
Essential genes in E. coliFirst results of an E. coli gene deletion project
ESTHEREsterases and other alpha/beta hydrolase enzymes
European rRNA databaseAll complete or nearly complete rRNA sequences
ExIntExon–intron structure of eukaryotic genes
EXProtSequences of proteins with experimentally verified function
Extra-TRAINExtragenic 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
FESDFunctional element SNPs database: SNPs located within promoters, UTRs, etc., of human genes
FGDBMIPS Fusarium graminearum genome database
FLIGHTInegrated data on Drosophila phenotypes, gene expression and protein interaction data
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
FlyTrapDrosophila mutants created using protein trap strategy
FlyViewDrosophila development and genetics
FREPFunctional repeats in mouse cDNAs
FSNFlexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool
Full-MalariaFull-length cDNA library from erythrocytic-stage Plasmodium falciparum
FUNPEPLow-complexity peptides capable of forming amyloid plaque
FunShiftFunctional divergence between the subfamilies of a protein domain family
FusionDBDatabase of bacterial and archaeal gene fusion events
GadFlyGenome annotation database of Drosophila
GALAGenomic alignment, annotation and experimental results
GDBHuman genes and genomic maps
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 Resource LocatorAlignment of ESTs with finished human sequence
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
GeneLocGene location database
GeneNestGene indices of human, mouse, zebrafish, etc.
GeneNoteHuman genes expression profiles in healthy tissues
GenePaintGene expression patterns in the mouse
Genetic CodesGenetic codes in various organisms and organelles
GeneTideA transcriptome-focused member of the GeneCards suite
GeneTrapExpression patterns in an embryonic stem library of gene trap insertions
GenewHuman gene nomenclature: approved gene symbols
GeniSysEnhancer- and promoter-inserted mutants of Drosophila
GenMapDBMapped human BAC clones
GenoBaseE. coli genome database at Nara Institute
GénolevuresA comparison of S. cerevisiae and 14 other yeast species
Genome AtlasDNA structural properties of sequenced genomes
Genome Information BrokerDDBJ’s collection of genome databases
Genome ReviewsIntegrated view of complete genomes
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: Gene expression profiles
Germline p53 MutationsMutations in human tumor and cell line p53 gene
GermOnlineGene expression in mitotic and meiotic cell cycle
GLIDAG-protein coupled receptors ligand database
GlycanCarbohydrate database, part of the KEGG system
GlycoSuiteDBN- and O-linked glycan structures and biological sources
GOGene ontology consortium database
GOAEBI’s gene ontology annotation project
GOLDGenomes online database: a listing of completed and ongoing genome projects
GOLD.dbGenomics of lipid-associated disorders database
GPCRDBG protein-coupled receptors database
gpDBG-proteins and their interaction with GPCRs
GRAPMutants of G-protein coupled receptors of family A
GRSDBG-rich sequences database
GTDGenomic threading database: Structural annotations of complete proteomes
GTOPProtein fold predictions from genome sequences
GtRDBGenomic tRNA database
Guide RNA DatabaseRNA editing in various kinetoplastid species
GXDMouse gene expression database
HaemBFactor IX gene mutations, insertions and deletions
HAGRHuman ageing genomic resources: Genes related to ageing in humans and model organisms
H-ANGELHuman anatomic gene expression library
HbVarHuman hemoglobin variants and thalassemias
HCADHuman chromosome aberration database: Chromosomal breakpoints and affected genes
HCVDBThe hepatitis C virus database
HemBaseGenes expressed in differentiating human erythroid cells
HemoPDBHematopoietic promoter database
HERVdHuman endogenous retrovirus database
Het-PDB NaviHetero-atoms in protein structures
HGMDHuman gene mutation database
HGT-DBPutative horizontally-transferred genes in prokaryotic genomes
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
HitsA database of protein domains and motifs
HIV Drug Resistance DatabaseHIV mutations that confer resistance to anti-HIV drugs
HIV Molecular Immunology DatabaseHIV epitopes
HIV RT and Protease Sequence DatabaseHIV reverse transcriptase and protease sequences
HIV Sequence DatabaseHIV RNA sequences
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 to
HOMSTRADHomologous structure alignment database: curated structure-based alignments for protein families
HoppsigenHuman and mouse homologous processed pseudogenes
HORDEHuman olfactory receptor data exploratorium
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
HTPSELEXTranscription factor binding site sequences obtained using high-throughput SELEX method
HUGEHuman unidentified gene-encoded large (>50 kDa) protein and cDNA sequences
HugeIndexExpression levels of human genes in normal tissues
HuGeMapHuman genome genetic and physical map data
Human BAC EndsNon-redundant human BAC end sequences
Human Genome Segmental Duplication DatabaseSegmental duplications in the human genome
Human p53/hprt, rodent lacI/lacZ databasesMutations at the human p53 and hprt genes; rodent transgenic lacI and lacZ mutations
Human PAX2 Allelic Variant DatabaseMutations in human PAX2 gene
Human PAX6 Allelic Variant DatabaseMutations in human PAX6 gene
HumHotHuman meiotic recombination hot spots
HUNTHuman novel transcripts: annotated full-length cDNAs
HuSiDaHuman siRNA database
HyPaLibHybrid pattern library: structural elements in classes of RNA
IARC TP53 DatabaseHuman TP53 somatic and germline mutations
ICBgyrB database for identification of bacteria
ICDSInterrupted coding sequences – frameshifts, stop codons, sequencing errors in microbial genomes
IGTCInternational mouse Gene Trap Consortium data
IMB Jena Image LibraryVisualization and analysis of 3D biopolymer structures
IMGIntergrated microbial genome database at the DOE Joint Genome Institute
IMGT/3Dstructure-DBSequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins
IMGT/PRIMER-DBImmunogenetics oligonucleotide primer database
IMOTdbSpatially interacting motif database
Imprinted Gene CatalogueImprinted genes and parent-of-origin effects in animals
InBaseInteins (protein splicing elements) database: properties, sequences, bibliography
INFEVERSHereditary inflammatory disorder and familial mediterranean fever mutation data
Influenza Virus ResourceProtein and nucleotide sequences of the influenza virus
InparanoidA database of eukaryotic orthologs
InsulatorDBInsulator regulatory elements in vertebrate genomes
IntAct projectProtein-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-protein interactions mediated by interchain beta-sheet formation
InterDomPutative protein domain interactions
InterProIntegrated resource of protein families, domains and functional sites
IntroneratorAlternative splicing in C. elegans and C. briggsae
IntroneratorIntrons and splicing in C. elegans and C. briggsae
INVHOGENHomologous invertebrate genes
IPDImmuno polymorphism database
IPIInternational protein index: human, mouse and rat proteins
iProClassIntegrated protein classification database
iProClassProtein families defined by PIR superfamilies and PROSITE patterns
IRESdbInternal ribosome entry site database
IRESiteExperimentally studied internal ribosome entry sites
ISfinderInsertion sequences from bacteria and archaea
IslanderPathogenicity islands and prophages in bacterial genomes
ISSDIntegrated sequence-structure database
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
IXDBPhysical maps of human chromosome X
JASPARPSSMs for transcription factor DNA-binding sites
JSNPJapanese SNP database
KaryotypeDBKaryotype and chromosome data for animal and plant species
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
KinG – Kinases in GenomesS/T/Y-specific protein kinases encoded in complete genomes
KinMutBaseDisease-causing protein kinase mutations
KlothoCollection and categorization of biological compounds
KnottinsDatabase 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
LeptoListLeptospira interrogans genome
LGICdbLigand-gated ion channel subunit sequences database
LIFEdbLocalization, interaction and functions of human proteins
LIGANDChemical compounds and reactions in biological pathways
Lipase Engineering DatabaseSequence, structure and function of lipases and esterases
Lipid MAPSLipid metabolites and pathways strategy
LOCATEMembrane organization and subcellular 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
MACiEMechanism, annotation and classification in enzymes: enzyme reaction mechanisms
MAGESTAscidian (Halocynthia roretzi) gene expression patterns
MAMEPMolecular anatomy of the mouse embryo project: Gene expression data on mouse embryos
Map ViewerDisplay of genomic information by chromosomal position
MAPPERPutative transcription factor binding sites in various genomes
MBGDMicrobial genome database for comparative analysis
MeGXMarine ecological genomix: genomics and metagenomics of marine bacteria
MEPDMedaka (freshwater fish Oryzias latipes) gene expression pattern database
MeRNAMetal ion binding sites in RNA
MEROPSDatabase of proteolytic enzymes (peptidases)
MetaCycMetabolic pathways and enzymes from various organisms
MetaGrowthGrowth requirements of bacterial pathogens
Metalloprotein SiteMetal-binding sites in metalloproteins
MetaRouterCompounds and pathways related to bioremediation
MethDBDNA methylation data, patterns and profiles
MFunGDMIPS mouse functional genomics database
MGCMammalian genome collection: Full-length ORFs for human, mouse, and rat genes
MICdbProkaryotic microsatellites
microRNA RegistryDatabase of microRNAs (small noncoding RNAs)
MIPSProtein databases at Munich Information Center for Protein Sequences
miRNAMapmicroRNA precursors and their mapping to targets in vertebrate genomes
MMDBNCBI’s database of 3D structures, part of NCBI Entrez
MNCDBMIPS Neurospora crassa database
Mobile group II intronsA database of group II introns, self-splicing catalytic RNAs
ModBaseAnnotated comparative protein structure models
MODOMICSA database of RNA modification pathways
MolliGenGenomic data on mollicutes
MolMovDBDatabase of macromolecular movements: Descriptions of protein and macromolecular motions, including movies
Monosaccharide BrowserSpace-filling Fischer projections of monosaccharides
Mouse Genome InformaticsFormerly mouse genome database
Mouse SAGESAGE libraries from various mouse tissues and cell lines
MpactYeast protein-protein interaction data
MPDBSynthetic oligonucleotides useful as primers or probes
MPromDBMammalian promoter database
MTBMouse tumor biology database: Tumor types, genes, classification, incidence, pathology
MtbRegListMycobacterium tuberculosis gene regulation
MTIDMouse transposon insertion database
MulPSSMMultiple PSSMs of structural and sequence families
NASCarraysNottingham Arabidopsis Stock Centre microarray database
NCBI Protein databaseAll protein sequences: translated from GenBank and imported from other protein databases
NCBI RefSeqNon-redundant collection of naturally-occurring biological molecules
NCBI TaxonomyNames of all organisms represented in GenBank
NCBI Viral GenomesViral genome resource at NCBI
NCIRNon-canonical interactions in RNA structures
NCL Mutation DatabasePolymorphisms 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
Nematode.netParasitic nematode sequencing project
NEMBASENematode sequence and functional data database
NESbaseNuclear export signals database
NetAffxPublic Affymetrix probesets and annotations
NLSdbNuclear localization signals
NMPdbNuclear matrix associated proteins database
NONCODEA database of noncoding RNAs
NOPdbNucleolar proteome database
NPDNuclear protein database
NPInterNoncoding RNA-protein interactions
NPRDNucleosome positioning region 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
Olfactory Receptor DatabaseSequences for olfactory receptor-like molecules
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
OncoMineCancer microarray data by gene or cancer type
ooTFDObject-oriented transcription factors database
Open Proteomics DatabaseMass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium
OPHIDOnline predicted human interaction database
Oral Cancer Gene DatabaseCellular and molecular data for genes involved in oral cancer
ORFanageDatabase of orphan ORFs (ORFs with no homologs) in complete microbial genomes
ORFDBCollection of ORFs that are sold by Invitrogen
OrthoMCLOrthologous protein clusters from multiple genomes
Osteo-Promoter DatabaseGenes in osteogenic proliferation and differentiation
PACRATArchaeal and bacterial intergenic sequence features
PA-GOSUBProtein sequences from model organisms, GO assignment and subcellular localization
PAHdbMutations at the phenylalanine hydroxylase locus
PALIPhylogeny and alignment of homologous protein structures
PANDITProtein and associated nucleotide domains with inferred trees
PANTHERGene products organized by biological function
ParaDBParalogy mapping in human genomes
PartiGeneDBAssembled partial genomes for ~250 eukaryotic organisms
PASS2Structural motifs of protein superfamilies
PathBaseEuropean mutant mice histopathology database: images
PathDBBiochemical pathways, compounds and metabolism
PathguideA listing of pathway, signal transduction and protein-protein interaction databases
PDBProtein structure databank: all publicly available 3D structures of proteins and nucleic acids
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
PDBrtfRepresentation of target families of enzymes in PDB
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
PEDBProstate expression database: ESTs from prostate tissue and cell type-specific cDNA libraries
PEDEPig EST data explorer: full-length cDNAs and ESTs
PEPPredictions for entire proteomes: Summarized analyses of protein sequences
PepConfDBA database of peptide conformations
PEPRPublic expression profiling resource: Expression profiles in a variety of diseases and conditions
PepSeekerPeptide identification and ion information from proteome experiments
PeptaibolPeptaibol (antibiotic peptide) sequences
PeptideAtlasPeptides identified in LC-MS/MS proteomics experiments
PfamProtein families: Multiple sequence alignments and profile hidden Markov models of protein domains
PGDBProstate and prostatic diseases gene database
PGTdbProkaryotic growth temperature database
PharmGKBPharmacogenomics knowledge base: effect of genetic variation on drug responses
PhenomicDBComparison of phenotypes of orthologous genes in human and model organisms
PHEXdbPHEX mutations causing X-linked hypophosphatemia
PHI-baseGenes affecting fungal pathogen-host interactions
Phospho.ELMS/T/Y protein phosphorylation sites (former PhosphoBase)
Phytophthora Functional Genomics DatabaseESTs and expression data from P. infestans and P. sojae
PINdbProteins interacting in nucleus (human and yeast)
PINTProtein-protein interactions thermodynamic database
PIR-ALNCurated database of protein sequence alignments
PIR-NREFPIR’s non-redundant reference protein database
PIRSFFamily/superfamily classification of whole proteins
PKRProtein kinase resource: sequences, enzymology, genetics and molecular and structural properties
PLACEPlant cis-acting regulatory DNA elements
Plant snoRNA DBsnoRNA genes in plant species
PlantCAREPlant promoters and cis-acting regulatory elements
PLANTncRNAsPlant non-coding RNAs
PlantPromPlant promoter sequences for RNA polymerase II
PlasmoDBPlasmodium genome database
PLPMDBPyridoxal-5′-phosphate dependent enzymes mutations
PMDCompilation of protein mutant data
PMDB3D protein models obtained from structure predictions
POINTPrediction of human protein-protein interactome
PolyA_DBA database of mammalian mRNA polyadenylation
PolymorphixA database of sequence polymorphisms
Poxvirus.orgPoxvirus genomic sequences and gene annotation
PPDProtein pKa database
PPNEMAPlant-parasitic nematode rRNAs
PRECISEPredicted and consensus interaction sites in enzymes
PRFProtein research foundation database of peptides: sequences, literature and unnatural amino acids
PRIDEProteomics identification database
PrimerPCRPCR primers for eukaryotic and prokaryotic genes
PRINTSHierarchical gene family fingerprints
probeBaserRNA-targeted oligonucleotide probe sequences, DNA microarray layouts, and associated information
ProDomProtein domain families
PRODORICProkaryotic database of gene regulation networks
ProLysEDA database 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
ProNITThermodynamic data on protein-nucleic acid interactions
PROPHECYProfiling of phenotypic characteristics in yeast
ProRuleFunctional and structural information on PROSITE profiles
PROSITEBiologically-significant protein patterns and profiles
Protein Folding DatabaseExperimental data on protein folding
Protein-protein interfacesInteracting residues in protein-protein interfaces in PDB
ProTeusSignature sequences at the protein N- and C-termini
ProThermThermodynamic data for wild-type and mutant proteins
ProtoMapHierarchical classification of Swiss-Prot proteins
ProtoNetHierarchical clustering of Swiss-Prot proteins
PseudoBaseDatabase of RNA pseudoknots
PseudoCAPPseudomonas aeruginosa genome database and community annotation project
PSIbaseInteraction of proteins with known 3D structures
PSORTdbProtein subcellular localization in bacteria
pSTIINGProtein signalling, transcriptional interactions and inflammation networks gateway
PTCH1 Mutation DatabaseMutations and SNPs found in PTCH1 gene
PubChemStructures and biological activities of small organic molecules
PubMedCitations and abstracts of biomedical literature
PUMA2Metabolic analysis of complete microbial genomes
QPPDQuantitative PCR Primer Database for human and mouse
QTL MatchmakerQuantitative trait loci mapping in human, mouse and rat
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
REBASERestriction enzymes and associated methylases
RECODEGenes using programmed translational recoding in their expression
RefExAReference database for human gene expression analysis
REFOLDExperimental data on protein refolding and purification
RegulonDBTranscriptional regulation and operon organization in E.coli
RESIDPre-, co- and post-translational protein modifications
RfamNon-coding RNA families
RHdbRadiation hybrid map data
Ribonuclease P DatabaseRNase P sequences, alignments and structures
RIDOMrRNA-based differentiation of medical microorganisms
RISSCRibosomal internal spacer sequence collection
RNA Modification DatabaseNaturally 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
RNRdbRibonucleotide reductase database
rOGEDRat ovarian gene expression database
RPGRibosomal protein gene database
RRNDBrRNA operon numbers in various prokaryotes
RsGDBRhodobacter sphaeroides genome
rSNP GuideSNPs in regulatory gene regions
RTCGDMouse retroviral tagged cancer gene database
RTKdbReceptor tyrosine kinase sequences
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
SDAPStructural database of allergenic proteins and food allergens
SELEX_DBDNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment
SENTRASensory signal transduction proteins
SEVENS7-transmembrane helix receptors (G-protein-coupled)
SGCEdbStructural genomics of C. elegans
SGDSaccharomyces genome database
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
siRNAdbFunctional human siRNA sequences
SitesBaseKnown ligand binding sites in the PDB
SKY/M-FISH and CGHFluorescent images of chromosomes and cytogenetic data
SloopClassification of protein loops
Small RNA DatabaseSmall RNAs from prokaryotes and eukaryotes
SMARTSimple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains
snoRNA-LBME-dbHuman C/D box and H/ACA modification guide RNAs
SNP Consortium databaseSNP Consortium data
SNP500CancerRe-sequenced SNPs from 102 reference samples
SNPeffectPhenotypic effects of human coding SNPs
SOURCEFunctional genomics resource for human, mouse and rat
SPDSecreted protein database
SpliceDBCanonical and non-canonical mammalian splice sites
SpliceInfoModes of alternative splicing in human genome
SpliceNestA tool for visualizing splicing of genes from EST data
SpodoBaseGenomics of the butterfly Spodoptera frugiperda
SRPDBSignal recognition particle database
SRPDBProteins of the signal recognition particles
SSU rRNA Modification DatabaseModified nucleosides in small subunit rRNA
STACKSequence tag alignment and consensus knowledgebase
Stanford Microarray DatabaseRaw and normalized data from microarray experiments
StellaBaseNematostella vectensis (sea anemone) genome
STING reportAmino acid properties in proteins of known structure
STRBaseShort tandem DNA repeats database
STRINGPredicted functional associations between proteins
Structure Superposition DatabasePairwise superposition of TIM-barrel structures
SubtiListBacillus subtilis genome database at Institut Pasteur
Subviral RNA DatabaseViroids and viroid-like RNAs
SuperDrug2D and 3D chemical structures of various drugs
SUPERFAMILYAssignments of proteins to structural superfamilies
SuperNaturalNatural compounds and their suppliers
SUPFAMGrouping of sequence families into superfamilies
SURFACESurface residues and functions annotated, compared and evaluated: a database of protein surface patches
SV40 Large T-Antigen MutantsMutations in SV40 large tumor antigen gene
SWEET-DBAnnotated carbohydrate structure and substance information
SWISS-2DPAGEAnnotated 2D gel electrophoresis database
SWISS-MODEL RepositoryDatabase of annotated 3D protein structure models
Swiss-ProtNow UniProt/SwissProt, part of the UniProt knowledgebase
SynDBSynaptic protein database
SYSTERSSystematic re-searching and clustering of proteins
T1DbaseA resource for type 1 diabetes research
T4-like genome databaseSequences of T4-like bacteriophages from various sources
TAEDThe adaptive evolution database: A phylogeny-based tool for comparative genomics
TargetDBTarget data from worldwide structural genomics projects
TBestDBTaxonomically broad EST database: protist ESTs
TCDBTransporter protein classification database
TcruziDBTrypanosoma cruzi genome database
TECRdbThermodynamics of enzyme-catalyzed reactions
TESSTranscription element search system
TGDTetrahymena thermophila genome
The Autism Chromosome Rearrangement DatabaseCurated collection of genomic features related to autism
The Chromosome 7 Annotation ProjectHuman chromosome 7 sequence and annotation
The Lafora DatabaseMutations and polymorphisms associated with Lafora progressive myoclonus epilepsy
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 Gene IndicesOrganism-specific databases of EST and gene sequences
TIGR Microbial DatabaseLists of completed and ongoing genome projects with links to complete genome sequences
TIGRFAMsTIGR protein families adapted for functional annotation
TiProDTissue-specific promoter database
TmaDBTissue microarray database
TMPDBExperimentally-characterized transmembrane topologies
tmRDBtmRNA database
tmRNA WebsitetmRNA sequences and alignments
Tooth Development DatabaseGene expression in dental tissue
TopoSNPTopographic database of non-synonymous SNPs
TOPSTopology of protein structures database
ToxoDBToxoplasma gondii genome database
TPMDTaiwan polymorphic microsatellite marker database
TRACTOR dbTranscription factors in gamma-proteobacteria database
TRANSCompel®Composite regulatory elements affecting gene transcription in eukaryotes
TRANSFAC®Transcription factors and binding sites
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
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 genes
TrEMBLNow UniProt/TrEMBL, part of the UniProt knowledgebase
TRIPLESTransposon-insertion phenotypes, localization, and expression in Saccharomyces
tRNA sequencestRNA viewer and sequence editor
trome, trEST and trGEN:Databases of predicted human protein sequences
TRRDTranscription regulatory regions of eukaryotic genes
TrSDBTranscription factor database
TTDTherapeutic target database
Tumor Gene Family DatabasesCellular, molecular and biological data about genes involved in various cancers
UCSC Archaeal Genome BrowserPyrococcus furiosus genome browser
UCSC Genome BrowserGenome assemblies and annotation
U-genomeGenome organization in unicellular eukaryotes
UM-BBDUniversity of Minnesota biocatalysis and biodegradation database
UMLSUnified medical language system
UniGeneNon-redundant set of eukaryotic gene-oriented clusters
UniGeneUnified clusters of ESTs and full-length mRNA sequences
UniParcUniProt archive, a repository of all protein sequences
UniProtUniversal protein knowledgebase
UniRefClustered sets of related sequences from UniProt
UniSTSUnified view of sequence tagged sites with mapping data
UniVecVector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contamination
UTRdb/UTRsite5′- and 3′-UTRs of eukaryotic mRNAs
VectorDBCharacterization and classification of nucleic acid vectors
VEGAVertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences
VIDAHomologous viral protein families database
VIPERdbVirus particle explorer: Virus capsid structures
Viral Bioinformatics Resource CenterVirus orthologous genes, gene families and genomes
VirFactBacterial virulence factors and pathogenicity islands
VirOligoVirus-specific oligonucleotides for PCR and hybridization
Virulence FactorsReference database for microbial virulence factors
VKCDBVoltage-gated potassium channel database
VMDVirginia Bioinformatics Institute microbial database
WILMAC. elegans annotation 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
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 introns.html
Yeast snoRNA DatabaseYeast small nucleolar RNAs
YEASTRACTYeast search for transcriptional regulators and consensus tracking
YGOBYeast gene order browser
yMGVYeast microarray global viewer
YRC PDRYeast resource center public data repository
ZFINZebrafish information network