Genomics Databases
Genomics Databases
genomics databases
|
Database name
|
Description
|
| Archaeal and bacterial ABC transporter database | |
| Nucleotide frequencies and the GC and TA skews in complete genome sequences | |
|
Clusters of orthologous groups of proteins
|
|
|
Complete genome tracking: predicted peptides from fully sequenced genomes |
|
|
Comparative regulatory genomics: conserved non-coding sequence blocks
|
|
|
Database of essential genes from bacteria and yeast
|
|
|
EBI's collection of databases for the analysis of complete and unfinished viral, prokaryotic and eukaryotic genomes |
|
|
Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices |
|
|
Enhanced microbial genomes library: completely sequenced genomes of
unicellular organisms
|
|
|
NCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
|
|
Light Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database |
|
|
Database of bacterial and archaeal gene fusion events
|
|
|
DNA structural properties of sequenced genomes
|
|
|
DDBJ's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
|
|
Integrated view of complete genomes
|
|
|
Genomes online database: a listing of completed and ongoing genome projects |
|
|
Putative horizontally transferred genes in prokaryotic genomes
|
|
| ICDS | Interrupted coding sequences - frameshifts, stop codons, sequencing errors in microbial genomes |
| IMG | Intergrated microbial genome database at the DOE Joint Genome Institute |
| INVHOGEN | Homologous invertebrate genes |
| ODB | Operon database |
|
Functional classification of proteins in whole genomes
|
|
|
Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins and metabolic pathways |
|
|
Microbial genome database for comparative analysis
|
|
|
Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes |
|
| Orthologous protein clusters from multiple genomes | |
|
Archaeal and bacterial intergenic sequence features
|
|
|
Assembled partial genomes for 250 eukaryotic organisms
|
|
|
Results of an automated analysis of genomic sequences
|
|
| PUMA2 | Metabolic analysis of complete microbial genomes |
| SIDDBase | Stress-induced DNA duplex destabilization profiles of complete microbial genomes |
|
Lists of completed and ongoing genome projects with links to complete genome sequences |
|
|
Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins |
|
|
Predicted membrane transporters in complete genomes, classified according to the TC classification system |
|
| TreeBase | Phylogenetic trees and the data matrices used to generate them |
| VMD | Virginia Bioinformatics Institute microbial database |
|
What is there? Metabolic reconstruction for completely sequenced microbial genomes |
Genome annotation terms, ontologies and nomenclature
|
Database name
|
Description
|
|
Human gene nomenclature: approved gene symbols
|
|
|
Gene ontology consortium database
|
|
|
EBI's gene ontology annotation project
|
|
|
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins |
|
|
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission |
|
|
The International Union of Pharmacology recommendations on receptor nomenclature and drug classification |
|
|
Gene products organized by biological function
|
|
|
Unified medical language system
|
Taxonomy and Identification
|
Database name
|
Description
|
|
gyrB database for identification and classification of bacteria
|
|
|
Names of all organisms represented in GenBank
|
|
|
Protein and associated nucleotide domains with inferred trees
|
|
|
rRNA-based differentiation of medical microorganisms
|
|
|
Ribosomal database project
|
|
|
Information on phylogeny and biodiversity
|
Organism-specific databases
| Database name | Description |
|
Descriptions of plant viruses |
|
|
The hepatitis C virus database |
|
|
HIV mutations that confer resistance to anti-HIV drugs |
|
|
HIV epitopes |
|
|
HIV reverse transcriptase and protease sequences |
|
|
Protein and nucleotide sequences of the influenza virus |
|
|
Viral genome resource at NCBI |
|
|
Poxvirus genomic sequences and gene annotation |
|
|
Sequences of T4-like bacteriophages from various sources |
|
|
Homologous viral protein families database |
|
|
Virus particle explorer: Virus capsid structures |
|
|
Virus orthologous genes, gene families and genomes |
|
|
Virus-specific oligonucleotides for PCR and hybridization |
Prokaryotes
| Database name | Description |
|
Picture atlas of annotated bacterial genomes |
|
|
Marine ecological genomix: genomics and metagenomics of marine bacteria |
|
|
Growth requirements of bacterial pathogens |
|
|
Prokaryotic growth temperature database |
Escherichia coli
| Database name | Description |
|
A systematic annotation package for community analysis of E. coli and related genomes |
|
|
A collection of data on E. coli K12 intended for mathematical modeling to simulate the bacterial cell |
|
|
A database for E. coli, Salmonella and Shigella |
|
|
E. coli genome database at Institut Pasteur |
|
|
Post-genomic studies of Escherichia coli |
|
|
First results of an E. coli gene deletion project |
|
|
E. coli genome database at Nara Institute |
|
|
E. coli K12 genome and proteome database |
|
|
Profiling of E. coli chromosome |
|
|
E. coli K12 genes, metabolic pathways, transporters, and gene regulation |
|
|
Sequence and literature data on E. coli genes and proteins |
|
|
Transcriptional regulation and operon organization in E.coli |
|
|
Shigella database |
Bacillus subtilis
| Database name | Description |
|
Bacillus subtilis genome database at Kyoto U. |
|
|
Non-redundant Bacillus subtilis database at U. Lyon |
|
|
Bacillus subtilis genome database at Institut Pasteur |
Other prokaryotes
| Database name | Description |
|
Pathway/genome databases for many bacteria |
|
|
Database for Campylobacter genome analysis |
|
|
Finished and unfinished genomes of Clostridium spp. |
|
|
Chlamydia Interactive Database: Gene expression data |
|
|
Cyanobacterial genomes |
|
|
Post-genome research of Listeria |
|
|
Leptospira interrogans genome |
|
|
Genomic data on mollicutes |
|
|
Mycobacterium tuberculosis gene regulation |
|
|
Pseudomonas aeruginosa genome database and community annotation project |
|
|
Rhodobacter sphaeroides genome |
|
|
Pyrococcus furiosus genome browser |
|
|
Bacterial virulence factors and pathogenicity islands |
|
|
Reference database for microbial virulence factors |
Unicellular eukaryotes
|
Database name |
Description |
|
EST sequences from various Apicomplexan parasites |
|
|
Cryptosporidium parvum genome database |
|
|
ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum |
|
|
Universal resource for Dictyostelium discoideum |
|
|
Full-length cDNA library from erythrocytic-stage Plasmodium falciparum |
|
|
Curated database for various Sanger-sequenced genomes |
|
|
ESTs of the earthworm Lumbricus rubellus |
|
|
Plasmodium genome database |
|
|
Taxonomically broad EST database: protist ESTs |
|
|
Trypanosoma cruzi genome database |
|
|
Toxoplasma gondii genome database |
|
|
Genome organization in unicellular eukaryotes |
Fungi
Yeasts
| Database name | Description |
|
Ashbya gossypii genome database |
|
|
Candida albicans genome database |
|
|
Candida albicans genome database |
|
|
MIPS Comprehensive yeast genome database |
|
|
A comparison of S. cerevisiae and 14 other yeast species |
|
|
Yeast protein-protein interaction data |
|
|
Profiling of phenotypic characteristics in yeast |
|
|
Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants |
|
|
Saccharomyces cerevisiae promoter database |
|
|
Saccharomyces genome database |
|
|
Transposon-insertion phenotypes, localization, and expression in Saccharomyces |
|
|
Yeast deletion project and mitochondria database |
|
|
Ares lab database of splicesomal introns in S. cerevisiae |
|
|
Yeast search for transcriptional regulators and consensus tracking |
|
|
Yeast small nucleolar RNAs |
|
|
Yeast gene order browser |
|
|
Yeast microarray global viewer |
|
|
Yeast resource center public data repository |
Other fungi
| Database name | Description |
|
Central Aspergillus data repository |
|
|
Phytopathogenic fungi and oomycete EST database |
|
|
MIPS Fusarium graminearum genome database |
|
|
MIPS Neurospora crassa database |
|
|
Oomycete Genomics Database: ESTs and annotation |
|
|
Genes affecting fungal pathogen-host interactions |
|
|
ESTs and expression data from P. infestans and P. sojae |
Invertebrates
Caenorhabditis elegans
| Database name | Description |
|
at the Sanger Institute |
|
|
Introns and splicing in C. elegans and C. briggsae |
|
|
RNAi phenotypic analysis of C. elegans genes |
|
|
Structural genomics of C. elegans |
|
|
C. elegans annotation database |
|
|
C. elegans ORFeome |
|
|
Data repository for C. elegans and C. briggsae: curated genome annotation, genetic and physical maps, pathways |
Drosophila melanogaster
| Database name | Description |
|
Inegrated data on Drosophila phenotypes, gene expression and protein interaction data |
|
|
Drosophila sequences and genomic information |
|
|
Database of the Drosophila nervous system |
|
|
Integration of insect genomic and proteomic data |
|
|
Genome-wide RNAi analysis data in Drosophila |
|
|
Drosophila mutants created using protein trap strategy |
|
|
Genome annotation database of Drosophila |
|
|
Enhancer- and promoter-inserted mutants of Drosophila |
|
|
Drosophila polymorphism database |
|
|
Data and tools for Drosophila gene expression studies |
|
|
Drosophila genes and their roles in development |
Other invertebrates
| Database name | Description |
|
A database on the nematode Pristionchus pacificus |
|
|
Genome database of the beetle Tribolium castaneum |
|
|
Macro- and micronuclear genes in spirotrichous ciliates |
|
|
Cnidarian evolution and gene expression database |
|
|
Parasitic nematode sequencing project |
|
|
Nematode sequence and functional data database |
|
|
Plant-parasitic nematode rRNAs |
|
|
Silkworm Bombyx mori ESTs, mutants, photographs |
|
|
A microsatellite database of the silkworm Bombyx mori |
|
|
Genomics of the butterfly Spodoptera frugiperda |
|
|
Nematostella vectensis (sea anemone) genome |
|
|
Tetrahymena thermophila genome database |