USEFUL DATABASES FOR ALL BIOPHILES
Genome Centers and Databases at the NCBI.
CORG: COmparative Regulatory Genomics Non-coding DNA segments database
fRNAdb: A portal site for functional RNAs and non-coding RNAs
SwissRegulon: Genome-wide annotations of regulatory sites in the intergenic regions
OriDB: DNA Replication Origin Database
NATsDB: Natural Antisense Transcripts DataBase
Pseudogene.org: Database for pseudogene annotation
PolymiRTS Database (Polymorphism in microRNA Target Site): A collection of naturally occurring DNA variations in putative microRNA target sites
SNPSTR: A database of microsatellite-SNP markers
GenomeTrafac: Transcription factor binding site clusters
SGDB: Synthetic Gene Database
TRDB: Tandem Repeats Database
REDIdb: RNA Editing Database
Snap: Single Nucleotide Polymorphism Annotation Platform
Patome DB: Biological sequence data disclosed in patents and published applications
Noncoding RNAs database (ncRNAdb)
PolyA_DB 2: mRNA polyadenylation sites
Ribosomal database project (RDP-II)
Sno/scaRNAbase: Small nucleolar RNAs and cajal body-specific RNAs
PReMod: Database of genome-wide cis-regulatory module (CRM) predictions
UCSC genome browser database
GenomeRNAi: RNAi phenotypes
U12DB: Database of orthologous U12-type spliceosomal introns
TRED: Transcriptional Regulatory Element Database
TassDB: TAndem Splice Site DataBase
GO PaD: Gene Ontology Partition Database
Universal Protein Resource (UniProt)
PIDD: Protein Inter-Atomic Distance Distribution Database
EVEREST: Evolutionarily conserved protein domains
SUBA: SubCellular Proteomic Database
Phospho3D: Database of three-dimensional structures of protein phosphorylation sites
FireDB: Fully automated search system for structures in the Protein Data Bank
TOPOFIT-DB: Database of protein structural alignments based on the TOPOFIT method
SUPERFAMILY database: Protein domain assignments
TMBETA-GENOME: beta-barrel membrane proteins
PANTHER version 6: Protein ANalysis THrough Evolutionary Relationships
Protein Folding Database (PFD 2.0): International Foldeomics Consortium
STRING 7: Protein–protein interactions
PeroxisomeDB: Database for the peroxisomal proteome, functional genomics and
disease
DisProt: Database of Disordered Proteins
Synapse protein DataBase
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid
proteomes
IntAct: Open source database system and analysis tools for protein interaction data
Michigan Molecular Interactions : Protein interactions
MINT: Molecular INTeraction database
PROTCOM: Database of protein complexes
SNAPPI-DB: Structures, iNterfaces and Alignments of Protein–Protein Interactions
DOMINO: Database of domain–peptide interactions
BindingDB: Binding affinities of protein–ligand complexes
eSLDB: Eukaryotic subcellular localization database
Human and Animals Related Database
PolyDoms: Mapping of Human Coding SNPs onto Protein Domains
SNP at Ethnos: Human SNPs and genes that contain human ethnic variation
Animal Genome Size Database AnimalQTLdb: Animal Quantitative Trait Loci (QTL) database
Mouse Gene Expression Database
MamPol: Mammalia Polymorphism Database
Mouse Genome Database
Pig Expression Data Explorer
Pig Genomic Informatics System
Rat Genome Database
VISTA Enhancer Browser: Database of tissue-specific human enhancers
ASAP II database: Comparative genomics of alternative splicing in 15 animal species
H-DBAS: Human-transcriptome DataBase for Alternative Splicing
miRGen: animal microRNA genomic organization
RNAdb 2.0: Mammalian non-coding RNAs
UniHI: Human protein interactome database
KBERG: KnowledgeBase for Estrogen Responsive Genes
HMDB: Human Metabolome Database
ECgene: Functional annotation of alternatively spliced genes
GeneSpeed database: Online database and resource tool for protein domain homology
PhenomicDB: Multi-species genotype/phenotype database
Virus Related Databases
euHCVdb: European hepatitis C virus database
HepSEQ: Repository for Hepatitis B
HIV positive selection mutation database
Influenza Virus Database (IVDB)
ViTa: Virus miRNA Target
MvirDB: LLNL Virulence Database
GIB-V: Genome Information Broker for Viruses
Pathogen Related Databases
MiST: Microbial Signal Transduction database
MBGD : Microbial Genome Database for Comparative analysis
National Microbial Pathogen Database Resource
Pristionchus.org: A database of the nematode satellite species Pristionchus pacificus
VectorBase: Invertebrate vectors of human pathogens
Fungal Genome Size Database
Tractor_DB (version 2.0) : A database of regulatory interactions in gamma-
proteobacterial genomes
Sentra: Database of signal transduction proteins encoded in completely sequenced prokaryotic genomes
Pathogenicity Island Database
RegTransBase: Database of regulatory sequences and interactions in prokaryotic
genomes
Candida albicans Genome Database
PATRIC: PathoSystems Resource Integration Center
Sulfolobus database
VNTRDB: Bacterial variable number tandem repeat locus database
Xanthusbase: Database for bacterium Myxococcus xanthus
dictyBase: Dictyostelium discoideum database
Comparasite: Database for comparative study of transcriptomes of parasites
ParameciumDB: Paramecium tetraurelia genome sequencing database
SYSTOMONAS: Systems Biology of Pseudomonas
PROPHECY: Yeast phenome database
BeetleBase: Red flour beetle (Tribolium castaneum) database
WormBase
Cancer and Immunology related Databases
CancerGenes
CYCLONET: Cell cycle regulation and carcinogenesis
OncoDB of hepatocellular carcinoma
PharmGED: Pharmacogenetic Effect Database
SuperHapten: Database for small immunogenic compounds
SISYPHUS: Structural alignments for proteins with non-trivial relationships
Defensins knowledgebase
Enzymes Related Databases
BRENDA, AMENDA and FRENDA: Enzyme information system
MACiE: A database of enzyme reaction mechanisms
CutDB: Proteolytic Event Database
CellCircuits: Molecular network models
Miscellaneous Databases
LMSD: LIPID MAPS Structure Database
TransportDB: Cytoplasmic membrane transporters and outer membrane channels
GlycoMapsDB: Database of the accessible conformational space of glycosidic linkages
TBestDB: A database of expressed sequence tags (ESTs)
GermOnline knowledgebase
D-HaploDB: Definitive Haplotype Database of Japanese complete hydatidiform moles
FINDbase: Frequency of INherited Disorders database
DIABETES DATABASES
T1DBase: A database of type 1 diabetes
EPConDB: A web resource for gene expression related to pancreatic development,
PLANT DATABASES
Gramene: A Resource for Comparative Grass Genomics
International Legume Database & Information Service
SOL Genomics Network: A genomics information resource for the Solanaceae family
PlantSat: A Database of plant satellite DNA
CSRDB: Cereal Small RNA Database
MIPSPlantsDB: Plant database resource for plant genome research
PathoPlant: A database on plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis
POGs/PlantRBP: Putative Orthologous Groups Plant RNA Binding Protein Database
ATTED: Arabidopsis thaliana trans-factor and cis-element prediction database
BASC: An integrated bioinformatics system for Brassica research
PlantQTL-GE: Identifying genes in rice and Arabidopsis by gene expression and QTL information
GABI-Kat SimpleSearch: Arabidopsis thaliana T-DNA mutant database
ForestTreeDB: Database of tree transcriptomes
MaizeGDB: Maize Genetics and Genomics Database
TomatEST database: Database of tomato EST sequences
RetrOryza: A database of the rice LTR-retrotransposons
GeneTrees: Phylogenomics resource for prokaryotes
Plant DNA C-values Database
AgBase: Functional analysis of agricultural plant and animal gene products