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1.Nucleotide Sequence Databases
1.1 International Nucleotide Sequence Database Collaboration
Database name
|
Full name and/or description
|
URL
|
DDBJ-DNA Data Bank of Japan
|
All known nucleotide and protein sequences
| |
EMBL-Nucleotide Sequence Database
|
All known nucleotide and protein sequences
| |
GenBank
|
All known nucleotide and protein sequences
|
1.2. DNA sequences: genes, motifs and regulatory sites
1.2.1. Coding and coding DNA
Database name
|
Full name and/or description
|
URL
|
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
| |
Imprinted Gene Catalogue
|
Imprinted genes and parent-of-origin effects in animals
| |
Islander
|
Pathogenicity islands and prophages in bacterial genomes
| |
MICdb
|
Prokaryotic microsatellites
| |
NPRD
|
Nucleosome positioning region database
| |
STRBase
|
Short tandem DNA repeats database
| |
TIGR Gene Indices
|
Organism-specific databases of EST and gene sequences
| |
Transterm
|
Codon usage, start and stop signals
| |
UniGene
|
Non-redundant set of eukaryotic gene-oriented clusters
| |
UniVec
|
Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination
| |
VectorDB
|
Characterization and classification of nucleic acid vectors
| |
Xpro
|
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron- less genes
|
1.2.2. Gene structure, introns and exons, splice sites
Database name
|
Full name and/or description
|
URL
|
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
| |
Intronerator
|
Alternative splicing in C.elegans and C.briggsae
| |
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
|
Database name
|
Full name and/or description
|
URL
|
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
| |
HemoPDB
|
Hematopoietic promoter database: transcriptional regulation in hematopoiesis
| |
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
|
E . coli promoters with experimentally identified transcriptional start sites
| |
SELEX_DB
|
DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment
| |
TESS
|
Transcription element search system
| |
TRACTOR db
|
Transcription factors in gamma-proteobacteria database
| |
TRANSCompel
|
Composite regulatory elements affecting gene transcription in eukaryotes
| |
TRANSFAC
|
Transcription factors and binding sites
| |
TRED
|
Transcriptional regulatory element database
| |
TRRD
|
Transcription regulatory regions of eukaryotic genes
|
2. RNA sequence databases
Database name
|
Full name and/or description
|
URL
|
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, proteins
| |
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
| |
Guide RNA Database
|
RNA editing in various kinetoplastid species
| |
HIV Sequence Database
|
HIV RNA sequences
| |
HuSiDa
|
Human siRNA database
| |
HyPaLib
|
Hybrid pattern library : structural elements in classes of RNA
| |
IRESdb
|
Internal ribosome entry site database
| |
microRNA Registry
|
Database of microRNAs (small non-coding RNAs)
| |
NCIR
|
Non-canonical interactions in RNA structures
| |
ncRNAs Database
|
Non-coding RNAs with regulatory functions
| |
NONCODE
|
A database of non-coding RNAs
| |
PLANTncRNAs
|
Plant non-coding RNAs
| |
Plant snoRNA DB
|
snoRNA genes in plant species
| |
PolyA_DB
|
A database of mammalian mRNA polyadenylation
| |
PseudoBase
|
Database of RNA pseudoknots
| |
Rfam
|
Non-coding RNA families
| |
RISSC
|
Ribosomal internal spacer sequence collection
| |
RNAdb
|
Mammalian non-coding RNA database
| |
RNA Modification Database
|
Naturally modified nucleosides in RNA
| |
RRNDB
|
rRNA operon numbers in various prokaryotes
| |
siRNAdb
|
siRNA database and search engine
| |
Small RNA Database
|
Small RNAs from prokaryotes and eukaryotes
| |
SRPDB
|
Signal recognition particle database
| |
SSU rRNA Modification Database
|
Modified nucleosides in small subunit rRNA
| |
Subviral RNA Database
|
Viroids and viroid-like RNAs
| |
tmRNA Website
|
tmRNA sequences and alignments
| |
tmRDB
|
tmRNA database
| |
tRNA sequences
|
tRNA viewer and sequence editor
| |
UTRdb/UTRsite
|
5' and 3' -UTRs of eukaryotic mRNAs
|
3. Protein sequence databases
3.1. General sequence databases
Database name
|
Full name and/or description
|
URL
|
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, TrEMBL and PIR protein sequence databases
| |
UniRef
|
UniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms)
|
3.2. Protein properties
Database name
|
Full name and/or description
|
URL
|
AAindex
|
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
|
3.3. Protein localization and targeting
Database name
|
Full name and/or description
|
URL
|
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
|
3.4. Protein sequence motifs and active sites
Database name
|
Full name and/or description
|
URL
|
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
| |
O-GlycBase
|
O- and C-linked glycosylation sites in proteins
| |
PDBSite
|
3D structure of protein functional sites
| |
Phospho.ELM
|
S/T/Y protein phosphorylation sites (formerly PhosphoBase)
| |
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
|
3.5. Protein domain databases; protein classification
Database name
|
Full name and/or description
|
URL
|
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 Markov models 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 and chromatin-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
|
3.6. Databases of individual protein families
Database name
|
Full name and/or description
|
URL
|
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
| |
DExH/D Family Database
|
DEAD-box, DEAH-box and DExH-box proteins
| |
Endogenous GPCR List
|
G protein-coupled receptors; expression in cell lines
| |
ESTHER
|
Esterases and other alpha/beta hydrolase enzymes
| |
EyeSite
|
Families of proteins functioning in the eye
| |
GPCRDB
|
G protein-coupled receptors database
| |
gpDB
|
G-proteins and their interaction with GPCRs
| |
Histone Database
|
Histone fold sequences and structures
| |
Homeobox Page
|
Homeobox proteins, classification and evolution
| |
Hox-Pro
|
Homeobox genes database
| |
Homeodomain Resource
|
Homeodomain sequences, structures and related genetic and genomic information
| |
HORDE
|
Human olfactory receptor data exploratorium
| |
InBase
|
Inteins (protein splicing elements) database: properties, sequences, bibliography
| |
KinG Kinases in Genomes
|
S/T/Y-specific protein kinases encoded in complete genomes
| |
Knottins
|
Database of knottins small proteins with an unusual disulfide through disulfide ' 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
| |
NucleaRDB
|
Nuclear receptor superfamily
| |
Nuclear Receptor Resource
|
Nuclear receptor superfamily
| |
NUREBASE
|
Nuclear hormone receptors database
| |
Olfactory Receptor Database
|
Sequences for olfactory receptor-like molecules
| |
ooTFD
|
Object-oriented transcription factors database
| |
PKR
|
Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties
| |
PLPMDB
|
Pyridoxal-5 0 -phosphate dependent enzymes mutations
| |
ProLysED
|
A database of bacterial protease systems
| |
Prolysis
|
Proteases and natural and synthetic protease inhibitors
| |
REBASE
|
Restriction enzymes and associated methylases
| |
Ribonuclease P Database
|
RNase P sequences, alignments and structures
| |
RPG
|
Ribosomal protein gene database
| |
RTKdb
|
Receptor tyrosine kinase sequences
| |
S/MARt dB
|
Nuclear scaffold/matrix attached regions
| |
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
| |
Wnt Database
|
Wnt proteins and phenotypes
|
4. Structure Databases
4.1. Small molecules
Database name
|
Full name and/or description
|
URL
|
ChEBI
|
Chemical entities of biological interest
| |
CSD
|
Cambridge structural database: crystal structure information for organic and metal-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
| |
Ligand Depot
|
Ligand Depot is a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules.
| |
PubChem
|
Structures and biological activities of small organic molecules
|
4.2. Carbohydrates
Database name
|
Full name and/or description
|
URL
|
CCSD
|
Complex carbohydrate structure database (CarbBank)
| |
CSS
|
Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB
| |
Glycan
|
Carbohydrate database, part of the KEGG system
| |
GlycoSuiteDB
|
N- and O-linked glycan structures and biological sources
| |
Monosaccharide Browser
|
Space-filling Fischer projections of monosaccharides
| |
SWEET-DB
|
Annotated carbohydrate structure and substance information
|
4.3. Nucleic acid structure
Database name
|
Full name and/or description
|
URL
|
NDB
|
Nucleic acid-containing structures
| |
NTDB
|
Thermodynamic data for nucleic acids
| |
RNABase
|
RNA-containing structures from PDB and NDB
| |
SCOR
|
Structural classification of RNA: RNA motifs by structure, function and tertiary interactions
|
4.4. Protein structure
Database name
|
Full name and/or description
|
URL
|
ArchDB
|
Automated classification of protein loop structures
| |
wwPDB
|
Worldwide Protein Data Bank
| |
PDBj
|
Protein Data Bank Japan-the archive for macromolecular 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 acids
| |
CADB
|
Conformational angles in proteins database
| |
CATH
|
Protein domain structures database
| |
CE 3D
|
protein structure alignments
| |
CKAAPs DB
|
Structurally similar proteins with dissimilar sequences
| |
Dali
|
Protein fold classification using the Dali search engine
| |
Decoys R' Us
|
Computer-generated protein conformations
| |
DisProt
|
Database of Protein Disorder: proteins that lack fixed 3D structure in their native states
| |
DomIns
|
Domain insertions in known protein structures
| |
DSDBASE
|
Native and modeled disulfide bonds in proteins
| |
DSMM
|
Database of simulated molecular motions
| |
eF-site
|
Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites
| |
GenDiS
|
Genomic distribution of protein structural superfamilies
| |
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
| |
HOMSTRAD
|
Homologous structure alignment database: curated structure-based alignments for protein families
| |
IMB Jena Image Library
|
Visualization and analysis of 3D biopolymer structures
| |
IMGT/3Dstructure-DB
|
Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins
| |
ISSD
|
Integrated sequence structure database
| |
LPFC
|
Library of protein family core structures
| |
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 and macromolecular 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 proteins and nucleic acids
| |
PDB-REPRDB
|
Representative protein chains, based on PDB entries
| |
PDBsum
|
Summaries and analyses of PDB structures
| |
PDB_TM
|
Transmembrane proteins with known 3D structure
| |
Protein Folding Database
|
Experimental data on protein folding
| |
SCOP
|
Structural classification of proteins
| |
Sloop
|
Classification of protein loops
| |
Structure Superposition Database
|
Pairwise superposition of TIM-barrel structures
| |
SWISS-MODEL Repository
|
Database of annotated 3D protein structure models
| |
SUPERFAMILY
|
Assignments of proteins to structural superfamilies
| |
SURFACE
|
Surface residues and functions annotated, compared and evaluated: a database 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
|
5. Genomics Databases (non-human)
5.1. Genome annotation terms, ontologies and nomenclature
Database name
|
Full name and/or description
|
URL
|
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 transport proteins and other proteins
| |
IUPAC Nomenclature database
|
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission
| |
IUPHAR-RD
|
The International Union of Pharmacology recommendations on receptor nomenclature and drug classification
| |
PANTHER
|
Gene products organized by biological function
| |
UMLS
|
Unified medical language system
|
5.1.1. Taxonomy and Identification
Database name
|
Full name and/or description
|
URL
|
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
| |
Tree of Life
|
Information on phylogeny and biodiversity
|
5.2. General genomics databases
Database name
|
Full name and/or description
|
URL
|
COG
|
Clusters of orthologous groups of proteins
| |
COGENT
|
Complete genome tracking: predicted peptides from fully sequenced genomes
| |
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 unfinished viral , pro- and eukaryotic genomes
| |
EGO
|
Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices
| |
EMGlib
|
Enhanced microbial genomes library: completely sequenced genomes of unicellular organisms
| |
Entrez Genomes
|
NCBI's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes
| |
ERGO
|
Light Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database
| |
FusionDB
|
Database of bacterial and archaeal gene fusion events
| |
Genome Atlas
|
DNA structural properties of sequenced genomes
| |
Genome Information Broker
|
DDBJ's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes
| |
Genome Reviews
|
Integrated view of complete genomes
| |
GOLD
|
Genomes online database: a listing of completed and ongoing genome projects
| |
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 on genes , proteins and metabolic pathways
| |
MBGD
|
Microbial genome database for comparative analysis
| |
ORFanage
|
Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes
| |
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 complete genome sequences
| |
TIGR Comprehensive Microbial Resource
|
Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins
| |
TransportDB
|
Predicted membrane transporters in complete genomes, classified according to the TC classification system
| |
WIT3
|
What is there ? Metabolic reconstruction for completely sequenced microbial genomes
|
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