Nucleotide Sequence Databases
DDBJ—DNA Data Bank of Japan	All known nucleotide and protein sequences
EMBL Nucleotide Sequence Database	All known nucleotide and protein sequences
GenBank1	All known nucleotide and protein sequences
DNA sequences: genes, motifs and regulatory sites
ACLAME	A classification of genetic mobile elements
CUTG	Codon usage tabulated from GenBank
Genetic Codes	Genetic codes in various organisms and organelles
Entrez Gene	Gene-centered information at NCBI
HERVd	Human endogenous retrovirus database
Hoppsigen	Human and mouse homologous processed pseudogenes
ACLAME	Imprinted genes and parent-of-origin effects in animals
CUTG	islands and prophages in bacterial genomes
Genetic Codes	Prokaryotic microsatellites
Entrez Gene	Nucleosome positioning region database
HERVd	Short tandem DNA repeats database
Hoppsigen	Gene Indices Organism-specific databases of EST and gene sequences
ACLAME	Codon usage, start and stop signals
CUTG	Non-redundant set of eukaryotic gene-oriented clusters
Genetic Codes	sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
ACLAME	Characterization and classification of nucleic acid vectors
CUTG	Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes
Gene structure, introns and exons, splice sites
ASAP	Alternative spliced isoforms
ASD	Alternative splicing database at EBI, includes three databases AltSplice,AltExtron and Aedb
ASDB	Alternative splicing database: protein products and expression patterns of alternatively spliced genes
ASHESdb	Alternatively spliced human genes by exon skipping database
EASED	Extended alternatively spliced EST database
ECgene	Genome annotation for alternative splicing
EDAS	EST-derived alternative splicing database
ExInt	Exon–intron structure of eukaryotic genes
HS3D	Homo sapiens splice sites dataset
SpliceDB	Canonical and non-canonical mammalian splice sites
SpliceInfo	Modes of alternative splicing in human genome
SpliceNest	A tool for visualizing splicing of genes from EST data
Transcriptional regulator sites and transcription factors
ACTIVITY	Functional DNA/RNA site activity
DBTBS	Bacillus subtilis promoters and transcription factors
DoOP	Database of orthologous promoters: chordates and plants
DPInteract	Binding sites for E.coli DNA binding proteins
EPD	Eukaryotic promoter database
JASPAR	PSSMs for transcription factor DNA-binding sites
MAPPER	Putative transcription factor binding sites in various genomes
PLACE	Plant cis-acting regulatory DNA elements
PlantCARE	Plant promoters and cis-acting regulatory elements
PlantProm	Plant promoter sequences for RNA polymerase II
PRODORIC	Prokaryotic database of gene regulation networks
PromEC	Ecoli promotors with experimentally identified transcriptional start sites
TESS	Transcription element search system
TRED	Transcriptional regulatory element database
RNA sequence databases
16S and 23S rRNA Mutation Database	16S and 23S ribosomal RNA mutations
5S rRNA Database	5S rRNA sequences
Aptamer database	Small RNA/DNA molecules binding nucleic acids, protein
ARED	AU-rich element-containing mRNA database
Mobile group II introns	A database of group II introns, self-splicing catalytic RNAs
European rRNA database	All complete or nearly complete rRNA sequences
GtRDB	Genomic tRNA database
HIV Sequence Database	HIV RNA sequences
HuSiDa	Human siRNA database
IRESdb	Internal ribosome entry site database
microRNA	Registry Database of microRNAs (small non-coding RNAs)
NONCODE	A database of non-coding RNAs
PLANTncRNAs	Plant non-coding RNAs
RNA Modification Database	Naturally modified nucleosides in RNA
RISSC	Ribosomal internal spacer sequence collection
RRNDB	rRNA operon numbers in various prokaryotes
Small RNA Database	Small RNAs from prokaryotes and eukaryotes
Protein sequence databases
EXProt	Sequences of proteins with experimentally verified function
NCBI Protein database	All protein sequences: translated from GenBank and imported from other protein databases
PA-GOSUB	Protein sequences from model organisms, GO assignment and subcellular localization
PIR-PSD	Protein information resource protein sequence database, has been merged into the UniProt knowledgebase
PIR-NREF	PIR’s non-redundant reference protein database
PRF	Protein research foundation database of peptides: sequences, literature and unnatural amino acids
Swiss-Prot	Now UniProt/Swiss-Prot: expertly curated protein sequence database,section of the UniProt knowledgebase
TrEMBL	Now UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase
UniParc	UniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence
UniProt	Universal protein knowledgebase: merged data from Swiss-Prot, TrEMBLand PIR protein sequence databases
UniRef	UniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms)
AA	index Physicochemical properties of amino acids
ProNIT	Thermodynamic data on protein–nucleic acid interactions
ProTherm	Thermodynamic data for wild-type and mutant proteins
TECRdb	Thermodynamics of enzyme-catalyzed reactions
DBSubLoc	Database of protein subcellular localization
NESbase	Nuclear export signals database
NLSdb	Nuclear localization signals
NMPdb	Nuclear matrix associated proteins database
NOPdb	Nucleolar proteome database
PSORTdb	Protein subcellular localization in bacteria
SPD	Secreted protein database
THGS	Transmembrane helices in genome sequences
TMPDB	Experimentally characterized transmembrane topologies
ASC	Active sequence collection: biologically active peptides
Blocks	Alignments of conserved regions in protein families
CSA	Catalytic site atlas: active sites and catalytic residues in enzymes of known  3D structure
COMe	Co-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins)
CopS	Comprehensive peptide signature database
eBLOCKS	Highly conserved protein sequence blocks
eMOTIF	Protein sequence motif determination and searches
Metalloprotein Site Database	Metal-binding sites in metalloproteins
PDBSite	3D structure of protein functional sites
PROMISE	Prosthetic centers and metal ions in protein active sites
PROSITE	Biologically significant protein patterns and profiles
ProTeus	Signature sequences at the protein N- and C-termini
ADDA	A database of protein domain classification
CDD	Conserved domain database, includes protein domains fromPfam, SMART,COG and KOG databases
CluSTr	Clusters of Swiss-Prot+TrEMBL proteins
FunShift	Functional divergence between the subfamilies of a protein domain family
Hits	A database of protein domains and motifs
InterPro	Integrated resource of protein families, domains and functional sites
iProClass	Integrated protein classification database
PIRSF	Family/superfamily classification of whole proteins
PRINTS	Hierarchical gene family fingerprints
Pfam	Protein families: multiple sequence alignments and profile hidden Markovmodels of protein domains
PRECISE	Predicted and consensus interaction sites in enzymes
ProDom	Protein domain families
ProtoMap	Hierarchical classification of Swiss-Prot proteins
ProtoNet	Hierarchical clustering of Swiss-Prot proteins
S4	Structure-based sequence alignments of SCOP superfamilies
SBASE	Protein domain sequences and tools
SMART	Simple modular architecture research tool: signalling, extracellular andchromatin-associated protein domains
SUPFAM	Grouping of sequence families into superfamilies
SYSTERS	Systematic re-searching and clustering of proteins
TIGRFAMs	TIGR protein families adapted for functional annotation
AARSDB	Aminoacyl-tRNA synthetase database
ASPD	Artificial selected proteins/peptides database
BacTregulators	Transcriptional regulators of AraC and TetR families
CSDBase	Cold shock domain-containing proteins
CuticleDB	Structural proteins of Arthropod cuticle
DCCP	Database of copper-chelating proteins
GPCRDB	G protein-coupled receptors database
Histone Database	Histone fold sequences and structures
Hox-Pro	Homeobox genes database
HORDE	Human olfactory receptor data exploratorium
KinG—	Kinases in Genomes S/T/Y-specific protein kinases encoded in complete genomes
Knottins	Database of knottins—small proteins with an unusual ‘disulfide throughdisulfide’ knot
LGICdb	Ligand-gated ion channel subunit sequences database
Lipase Engineering Database	Sequence, structure and function of lipases and esterases
LOX-DB	Mammalian, invertebrate, plant and fungal lipoxygenases
MEROPS	Database of proteolytic enzymes (peptidases)
NPD	Nuclear protein database
NUREBASE	Nuclear hormone receptors database
Olfactory Receptor Database	Sequences for olfactory receptor-like molecules
ooTFD	Object-oriented transcription factors database
ProLysED	A database of bacterial protease systems
Prolysis	Proteases and natural and synthetic protease inhibitors
RPG	Ribosomal protein gene database
RTKdb	Receptor tyrosine kinase sequences
Scorpion	Database of scorpion toxins
SDAP	Structural database of allergenic proteins and food allergens
SENTRA	Sensory signal transduction proteins
SEVENS	7-transmembrane helix receptors (G-protein-coupled)
SRPDB	Proteins of the signal recognition particles
TrSDB	Transcription factor database
VKCDB	Voltage-gated potassium channel database
Structure Databases
ChEBI	Chemical entities of biological interest
CSD	Cambridge structural database: crystal structure information for organic andmetal-organic compounds
HIC-Up	Hetero-compound Information Centre—Uppsala
AANT	Amino acid–nucleotide interaction database
Klotho	Collection and categorization of biological compounds
LIGAND	Chemical compounds and reactions in biological pathways
PDB-Ligand	3D structures of small molecules bound to proteins and nucleic acids
PubChem	Structures and biological activities of small organic molecules
CCSD	Complex carbohydrate structure database (CarbBank)
SWEET-DB	Annotated carbohydrate structure and substance information
NDB	Nucleic acid-containing structures
RNABase	RNA-containing structures from PDB and NDB
SCOR	Structural classification of RNA: RNA motifs by structure, function andtertiary interactions
ArchDB	Automated classification of protein loop structures
ASTRAL	Sequences of domains of known structure, selected subsets and sequence–structure correspondences
BAliBASE	A database for comparison of multiple sequence alignments
BioMagResBank	NMR spectroscopic data for proteins and nucleic acid
CADB	Conformational angles in proteins database
CATH	Protein domain structures database
CE	3D protein structure alignments
Dali	Protein fold classification using the Dali search engine
DisProt	Database of Protein Disorder: proteins that lack fixed 3D structure in theirnative states
DomIns	Domain insertions in known protein structures
DSDBASE	Native and modeled disulfide bonds in proteins
DSMM	Database of simulated molecular motions
Gene3D	Precalculated structural assignments for whole genomes
GTD	Genomic threading database: structural annotations of complete proteomes
GTOP	Protein fold predictions from genome sequences
Het-PDB Navi	Hetero-atoms in protein structures
IMGT/3Dstructure	DB Sequences and 3D structures of vertebrate immunoglobulins, T cellreceptors and MHC proteins
ISSD	Integrated sequence–structure database
MMDB	NCBI’s database of 3D structures, part of NCBI Entrez
E-MSD	EBI’s macromolecular structure database
ModBase	Annotated comparative protein structure models
MolMovDB	Database of macromolecular movements: descriptions of protein andmacromolecular motions, including movies
PALI	Phylogeny and alignment of homologous protein structures
PASS2	Structural motifs of protein superfamilies
PepConfDB	A database of peptide conformations
PDB Protein structure databank	all publicly available 3D structures of proteinsand nucleic acids
PDBsum	Summaries and analyses of PDB structures
PDB_TM	Transmembrane proteins with known 3D structure
SCOP	Structural classification of proteins
SWISS-MODEL Repository	Database of annotated 3D protein structure models
SURFACE	Surface residues and functions annotated, compared and evaluated: adatabase of protein surface patches
TargetDB	Target data from worldwide structural genomics projects
3D-GENOMICS	Structural annotations for complete proteomes
TOPS	Topology of protein structures database
Genomics Databases (non-human)
Genew	Human gene nomenclature: approved gene symbols
GO	Gene ontology consortium database
GOA	EBI’s gene ontology annotation project
IUBMB Nomenclature database	Nomenclature of enzymes, membrane transporters, electron transportproteins and other proteins
IUPAC Nomenclature database	Nomenclature of biochemical and organic compounds approved by theIUBMB-IUPAC Joint Commission
IUPHAR-RD	The International Union of Pharmacology recommendations on receptornomenclature and drug classification
PANTHER	Gene products organized by biological function
UMLS	Unified medical language system
Taxonomy and Identification
ICB gyrB	database for identification and classification of bacteria
NCBI	Taxonomy Names of all organisms represented in GenBank
PANDIT	Protein and associated nucleotide domains with inferred trees
RIDOM	rRNA-based differentiation of medical microorganisms
RDP-II	Ribosomal database project
General genomics databases
COG	Clusters of orthologous groups of proteins
COGENT	Complete genome tracking: predicted peptides from fully sequencedgenomes
CORG	Comparative regulatory genomics: conserved non-coding sequence blocks
DEG	Database of essential genes from bacteria and yeast
EBI	Genomes EBI’s collection of databases for the analysis of complete and unfinishedviral, pro- and eukaryotic genomes
EGO	Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR geneindices
EMGlib	Enhanced microbial genomes library: completely sequenced genomes ofunicellular organisms
Entrez Genomes	NCBI’s collection of databases for the analysis of complete and unfinishedviral, pro- and eukaryotic genomes
ERGOLight	Integrated biochemical data on nine bacterial genomes: publicly availableportion of the ERGO database
FusionDB	Database of bacterial and archaeal gene fusion events
DDBJ’s	collection of databases for the analysis of complete and unfinishedviral, pro- and eukaryotic genomes
GOLD	Genomes online database: a listing of completed and ongoing genomeprojects
HGT-DB	Putative horizontally transferred genes in prokaryotic genomes
Integr8	Functional classification of proteins in whole genomes
KEGG	Kyoto encyclopedia of genes and genomes: integrated suite of databases ongenes, proteins and metabolic pathways
MBGD	Microbial genome database for comparative analysis
PACRAT	Archaeal and bacterial intergenic sequence features
PartiGeneDB	Assembled partial genomes for 250 eukaryotic organisms
PEDANT	Results of an automated analysis of genomic sequences
TIGR	Microbial Database Lists of completed and ongoing genome projects with links to completegenome sequences
TIGR	Various data on complete microbial genomes: uniform annotation,properties of DNA and predicted proteins
TransportDB	Predicted membrane transporters in complete genomes classified accordingto the TC classification system
WIT3	What is there? Metabolic reconstruction for completely sequenced microbial genomes
Organism-specific databases
Viruses
HCVDB	The hepatitis C virus database
HIV Drug Resistance Database	HIV mutations that confer resistance to anti-HIV drugs
T4-like genome database	Sequences of T4-like bacteriophages from various sources
VIDA	Homologous viral protein families database
VIPER	Virus particle explorer: virus capsid structures
VirOligo	Virus-specific oligonucleotides for PCR and hybridization
Prokaryotes
BacMap	Picture atlas of annotated bacterial genomes
MetaGrowth	Growth requirements of bacterial pathogens
PGTdb	Prokaryotic growth temperature database
Escherichia coli
ASAP	A systematic annotation package for community analysis of E.coli and related genomes
CyberCell database	A collection of data on E.Coli K.1.2 intented for mathematical modelling to stimule bacterial cell.l
coliBase	A database for E.coli, salmonella
Colibri	E.coli genome at Institute Pasteur
EchoBASE	Post-genomic studies of E.coli
GenoBase	E.coli genome database at Nara Institute
GenProtEC	E.coli K12 genome and proteome database
PEC	Profiling of E.coli chromosome
EcoCyc	E.coli K12 genes, metabolic pathways, transporters and gene regulation
RegulonDB	Transcriptional regulation and operon organization in E.coli
Bacillus subtilis
BSORF	Bacillus subtilis genome database at kyoto
NRSub	Non-redundant Bacillus subtilis database at U.Lyon
Other bacteria
BioCyc	Pathway/genome databases for many bacteria
CampyDB	Database for Campylobacter genome analysis
ClostriDB	Finished and unfinished genomes of Clostridium spp.
CIDB	Chlamydia Interactive database: gene expression data
CyanoBase	Cyanobacterial genomes
LeptoList	Leptospira interrogans genome
MolliGen	Genomic data on mollicutes
PseudoCAP	Pseudomonas aeruginosa genome database
RsGDB	Rhodobacter sphaeroides genome
VirFact	Bacterial virulence factors and pathogenicity islands
Virulence Factors	Reference database for microbial virulence factors
Unicellular eukaryotes
ApiEST-DB	EST sequences from various Apicomplexan parasites
CryptoDB	Cryptosporidium parvum genome database
Diatom EST	Database ESTs from two diatom algae,Thalassiosira pseudonana and Phaeodactylum tricornutum
DictyBase	Universal resource for Dictyostelium discoideum
GeneDB	Curated database for various Sanger-sequenced genomes
LumbriBASE	ESTs of the earthworm Lumbricus rubellus
PlasmoDB	Plasmodium genome database
TcruziDB	Trypanosoma cruzi genome database
ToxoDB	Toxoplasma gondii genome database
Fungi
AGD	Ashbya gossypii genome database
CandidaDB	Candida albicans genome database
CYGD MIPS	Comprehensive yeast genome database
Ge´nolevures	A comparison of S.cerevisiae and 14 other yeast sp.
PROPHECY	Profiling of phenotypic characteristics in yeast
SCMD	Saccharomyces cerevisiae morphological database
SCPD	Saccharomyces cerevisiae promotor database
TRIPLES	Transposon-insertion phenotypes, localization and expression in Saccharomyces
Yeast snoRNA Database	Yeast small nucleolar RNAs
Invertebrates
RNAiDB	RNAi phenotypic analysis of  C.elegans genes
WILMA	C.elegans annotation database
WormBase	Data repository for C.elegans and C.briggsae: curated genome annotation, genetics, physical map
Drosophila melanogaster
FlyBase	Drosophila sequence and genomic informations
FlyBrain	Database of the Drosophila nervous system
FlyMine	Integration of insect genomic and proteomic data
FlyTrap	Drosophila mutants created using GFP protein trap strategy
GadFly	Genome annotation database of Drosophila
DPDB	Drosophila polymorphism database
Other invertebrates
AppaDB	A database on the nematode Pristionchus pacificus
BeetleBase	Genome database of the beetle Tribolium castaneum
CnidBase	Cnidarian evolution and gene expression database
Nematode.net	Parasitic nematode sequencing project
NEMBASE	Nematode sequence and functional data database
PPNEMA	Plant-parasitic nematode rRNAs
SilkDB	Silkworm Bombyx mori ESTs, mutants, photographs.
SilkSatDb	A microsatellite database of the silkworm Bombyx mori
Metabolic Enzymes and Pathways database
BRENDA	Enzyme names and biochemical properties
ENZYME	Enzyme nomenclature and properties
EzCatDB	Enzyme Catalytic Mechanism Database
IntEnz	Integrated enzyme database and enzyme nomenclature
PDBrtf	Representation of target families of enzymes in PDB
SCOPEC	Mapping of catalytic function to domain structure
BioSilico	Integrated access to various metabolic databases
KEGG	Pathway Metabolic and regulatory pathways in complete genomes
MetaCyc	Metabolic pathways and enzymes from various organisms
PathDB	Biochemical pathways, compounds and metabolism
UM-BBD	University of Minnesota biocatalysis and biodegradation database
aMAZE	A system for the annotation, management, and analysis of biochemical andsignalling pathway networks
BIND	Biomolecular interaction network database
BioCarta	Online maps of metabolic and signaling pathways
BRITE	Biomolecular relations in information transmission and expression, part of KEGG
DDIB	Database of domain interactions and binding
GeneNet	Database on gene network components
HPID	Human protein interaction database
InterDom	Putative protein domain interactions
PDZBase	Protein–protein interactions involving PDZ domains
POINT	Prediction of human protein–protein interactome
PSIbase	Interaction of proteins with known 3D structures
Reactome	A knowledgebase of biological pathways
STCDB	Signal transductions classification database
STRING	Predicted functional associations between proteins
TRANSPATH	Gene regulatory networks and microarray analysis