Bioinformatics Database
AgBase: Functional analysis of agricultural plant and animal
gene products
Animal Genome Size Database
AnimalQTLdb: Animal Quantitative Trait Loci (QTL) database
ASAP II database: Comparative genomics of alternative splicing
in 15 animal species
BeetleBase: Red flour beetle (Tribolium castaneum) database
BindingDB: Binding affinities of protein–ligand complexes
BRENDA, AMENDA and FRENDA: Enzyme information system
CancerGenes
Candida albicans Genome Database
CellCircuits: Molecular network models
Click here! To view Genome Centers and Databases at the NCBI.
Comparasite: Database for comparative study of transcriptomes of
parasites
CORG: COmparative Regulatory Genomics Non-coding DNA segments
database
CutDB: Proteolytic Event Database
CYCLONET: Cell cycle regulation and carcinogenesis
Defensins knowledgebase
D-HaploDB: Definitive Haplotype Database of Japanese complete
hydatidiform moles
dictyBase: Dictyostelium discoideum database
DisProt: Database of Disordered Proteins
DOMINO: Database of domain–peptide interactions
ECgene: Functional annotation of alternatively spliced genes
eSLDB: Eukaryotic subcellular localization database
euHCVdb: European hepatitis C virus database
EVEREST: Evolutionarily conserved protein domains
FINDbase: Frequency of INherited Disorders database
FireDB: Fully automated search system for structures in the
Protein Data Bank
fRNAdb: A portal site for functional RNAs and non-coding RNAs
Fungal Genome Size Database
GeneSpeed database: Online database and resource tool for
protein domain homology
GeneTrees: Phylogenomics resource for prokaryotes
GenomeRNAi: RNAi phenotypes
GenomeTrafac: Transcription factor binding site clusters
GermOnline knowledgebase
GIB-V: Genome Information Broker for Viruses
GlycoMapsDB: Database of the accessible conformational space of
glycosidic linkages
GO PaD: Gene Ontology Partition Database
H-DBAS: Human-transcriptome DataBase for Alternative Splicing
HepSEQ: Repository for Hepatitis B
HIV positive selection mutation database
HMDB: Human Metabolome Database
Influenza Virus Database (IVDB)
IntAct: Open source database system and analysis tools for
protein interaction data
KBERG: KnowledgeBase for Estrogen Responsive Genes
LMSD: LIPID MAPS Structure Database
MACiE: A database of enzyme reaction mechanisms
MamPol: Mammalia Polymorphism Database
MAPU: Max-Planck Unified database of organellar, cellular,
tissue and body fluid proteomes
MBGD: Microbial Genome Database for Comparative analysis
Michigan Molecular Interactions : Protein interactions
MINT: Molecular INTeraction database
miRGen: animal microRNA genomic organization
MiST: Microbial Signal Transduction database
Mouse Gene Expression Database
Mouse Genome Database
MvirDB: LLNL Virulence Database
National Microbial Pathogen Database Resource
NATsDB: Natural Antisense Transcripts DataBase
Noncoding RNAs database (ncRNAdb)
OncoDB of hepatocellular carcinoma
OriDB: DNA Replication Origin Database
PANTHER version 6: Protein ANalysis THrough Evolutionary
Relationships
ParameciumDB: Paramecium tetraurelia genome sequencing database
Pathogenicity Island Database
Patome DB: Biological sequence data disclosed in patents and
published applications
PATRIC: PathoSystems Resource Integration Center
PEDANT genome database
PeroxisomeDB: Database for the peroxisomal proteome, functional
genomics and disease
PharmGED: Pharmacogenetic Effect Database
PhenomicDB: Multi-species genotype/phenotype database
Phospho3D: Database of three-dimensional structures of protein
phosphorylation sites
PIDD: Protein Inter-Atomic Distance Distribution Database
Pig Expression Data Explorer
Pig Genomic Informatics System
Plant DNA C-values Database
PolyA_DB 2: mRNA polyadenylation sites
PolyDoms: Mapping of Human Coding SNPs onto Protein Domains
PolymiRTS Database (Polymorphism in microRNA Target Site): A
collection of naturally occurring DNA variations in putative
microRNA target sites
PReMod: Database of genome-wide cis-regulatory module (CRM)
predictions
Pristionchus.org: A database of the nematode satellite species
Pristionchus pacificus
PROPHECY: Yeast phenome database
PROTCOM: Database of protein complexes
Protein Folding Database (PFD 2.0): International Foldeomics
Consortium
Pseudogene.org: Database for pseudogene annotation
Rat Genome Database
REDIdb: RNA Editing Database
RegTransBase: Database of regulatory sequences and interactions
in prokaryotic genomes
RetrOryza: A database of the rice LTR-retrotransposons
Ribosomal database project (RDP-II)
RNAdb 2.0: Mammalian non-coding RNAs
Sentra: Database of signal transduction proteins encoded in
completely sequenced prokaryotic genomes
SGDB: Synthetic Gene Database
SISYPHUS: Structural alignments for proteins with non-trivial
relationships
Snap: Single Nucleotide Polymorphism Annotation Platform
SNAPPI-DB: Structures, iNterfaces and Alignments of
Protein–Protein Interactions
Sno/scaRNAbase: Small nucleolar RNAs and cajal body-specific
RNAs
SNP at Ethnos: Human SNPs and genes that contain human ethnic
variation
SNPSTR: A database of microsatellite-SNP markers
STRING 7: Protein–protein interactions
SUBA: SubCellular Proteomic Database
Sulfolobus database
SUPERFAMILY database: Protein domain assignments
SuperHapten: Database for small immunogenic compounds
SwissRegulon: Genome-wide annotations of regulatory sites in the
intergenic regions
Synapse protein DataBase
SYSTOMONAS: Systems Biology of Pseudomonas
TassDB: TAndem Splice Site DataBase
TBestDB: A database of expressed sequence tags (ESTs)
TMBETA-GENOME: beta-barrel membrane proteins
TOPOFIT-DB: Database of protein structural alignments based on
the TOPOFIT method
Tractor_DB (version 2.0): A database of regulatory interactions
in gamma-proteobacterial genomes
TransportDB: Cytoplasmic membrane transporters and outer
membrane channels
TRDB: Tandem Repeats Database
TRED: Transcriptional Regulatory Element Database
U12DB: Database of orthologous U12-type spliceosomal introns
UCSC genome browser database
UniHI: Human protein interactome database
Universal Protein Resource (UniProt)
VectorBase: Invertebrate vectors of human pathogens
VISTA Enhancer Browser: Database of tissue-specific human
enhancers
ViTa: Virus miRNA Target
VNTRDB: Bacterial variable number tandem repeat locus database
WormBase :Data base for worm
Xanthusbase: Database for bacterium Myxococcus xanthus
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