[转载]基因组学数据库(非人类)
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5. Genomics Databases (non-human) |
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5.1. Genome annotation terms, ontologies and nomenclature |
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BioThesaurus |
A collection of gene/protein names and associated sequences |
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FunSimMat |
Gene Ontology-based functional similarity values for proteins and protein families |
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GO |
Gene ontology consortium database |
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GOA |
Gene Ontology Annotation |
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GOPaD |
Gene Ontology Partition Database |
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HGNC Database |
The HUGO Gene Nomenclature Database (formerly Genew) |
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IUBMB Nomenclature database |
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins |
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IUPAC Nomenclature database |
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission |
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IUPHAR-RD |
International Union of Pharmacology recommendations on receptor nomenclature and drug classification |
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Plant Ontology DB |
Controlled vocabulary of plant structures and growth stages |
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SOURCE |
Functional genomics resource for human, mouse and rat |
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TreeBase |
Phylogenetic trees and the data matrices used to generate them |
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UMLS |
Unified medical language system |
Requires user registration |
| 5.2. Taxonomy and identification | ||
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GeneTrees |
Pre-compiled alignments and gene phylogenies for a variety of taxonomic groups |
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ICB |
gyrB database for identification of bacteria |
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IDBD |
Infectious Disease Biomarker Database |
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NCBI Taxonomy Browser |
Names of all organisms that are represented in GenBank |
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RIDOM |
Ribosomal Differentiation of Medical Microorganisms |
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SuperCAT |
Database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria |
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Tree of Life |
Information on phylogeny and biodiversity |
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VNTR Locus DB |
Bacterial Variable Number Tandem Repeat locus database |
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| 5.3. General genomics databases | ||
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BacMap |
Picture atlas of annotated bacterial genomes |
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CoGenT++ |
Complete genome tracking: Predicted peptides from fully sequenced genomes |
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DEG |
Database of Essential Genes |
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diArk |
Database of eukaryotic sequencing projects |
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EBI Genomes |
EBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
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Entrez Genomes |
NCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
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ERGO-Light |
Integrated biochemical data on 10 bacterial genomes: Publicly-available portion of the ERGO database |
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GenDiS |
Genomic distribution of protein structural superfamilies |
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GeneNest |
Gene indices of human, mouse, zebrafish, etc. |
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GenoList |
An integrated environment for comparative analysis of microbial genomes |
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Genome Information Broker |
DDBJ's collection of genome databases |
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Genome Reviews |
Integrated view of complete genomes |
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Genome Project DB |
NCBI's database of large-scale genome sequencing projects |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj |
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GOLD |
Genomes online database: a listing of completed and ongoing genome projects |
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HOINVGEN |
Homologous invertebrate genes |
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Inparanoid |
Database of eukaryotic orthologs |
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Integr8 |
Functional classification of proteins in whole genomes |
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KaryotypeDB |
Karyotype and chromosome data for animal and plant species |
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KEGG |
Kyoto Encyclopedia of Genes and Genomes: databases on genes, proteins, and metabolic pathways |
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MBGD |
Microbial genome database for comparative analysis |
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MetaCyc |
Metabolic pathways and enzymes from various organisms |
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Narcisse |
Conserved syntenies for various animal, plant and bacterial genomes |
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NegProt |
Negative Proteome: A tool for comparison of complete proteomes |
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NMPDR |
Database for functional annotation and comparative analysis of microbial genomes |
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OPTIC |
Orthologous and Paralogous Transcripts in Clades |
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ORFanage |
Orphan ORFs (ORFs with no homologs) in microbial genomes |
No longer maintained |
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OrthoDB |
An hierarchical catalog of orthologous proteins in metazoa |
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OrthoMCL |
Orthologous protein clusters from multiple genomes |
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PartiGeneDB |
Assembled partial genomes for ~250 eukaryotic organisms |
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PEDANT |
Results of an automated analysis of genomic sequences |
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PEP |
Predictions for Entire Proteomes |
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PhylomeDB |
Experimentally validated and predicted serine phosphorylation sites inArabidopsis thaliana |
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PUMA2 |
Metabolic analysis of complete microbial genomes |
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STRING |
Predicted functional associations between proteins |
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TIGR Comprehensive Microbial Resource |
Various data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteins |
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TIGR Gene Indices |
Organism-specific databases of EST and gene sequences |
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TIGR Microbial DB |
A list of microbial genome sequencing projects |
No longer maintained |
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VBI Microbial Database |
Virginia Bioinformatics Institute microbial database |
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5.4. Viral genome databases |
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BioHealthBase |
Host-pathogen interactions of influenza virus |
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CoVDB |
Database of coronavirus genes and genomes |
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DPVweb |
Descriptions of plant viruses |
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euHCVdb |
European Hepatitis C Virus database |
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HCV Database |
Hepatitis C Virus (HCV) Sequence Database |
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HCVdb |
Hepatitis C Virus Database |
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HepSeq |
Epidemiological, clinical, and sequence data on the Hepatitis B virus |
http://www.hpa-bioinfodatabases.org.uk/ hepatitis_open/main.php |
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HERVd |
Human Endogenous Retrovirus database |
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HIV Drug Resistance Database |
HIV mutations that confer resistance to anti-HIV drugs |
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HIV Molecular Immunology Database |
HIV epitopes |
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HIV Positive Selection Mutation Database |
Positively selected mutations in HIV-1 protease and reverse transcriptase |
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Influenza Virus Resource |
Protein and nucleotide sequences of the influenza virus |
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IVDB |
Influenza Virus Database : Annotated sequences and geographic distribution of the influenza virus |
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NCBI Viral Genomes |
Viral genome resource at NCBI |
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Poxvirus.org |
Poxvirus genomic sequences and gene annotation |
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T4-like genome DB |
Sequences of T4-like bacteriophages from various sources |
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VIDA |
Homologous viral protein families database |
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VIPERdb |
Virus particle explorer: Virus capsid structures |
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Viral Bioinformatics Resource Center |
Virus orthologous genes, gene families and genomes |
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VirGen |
Curated database for complete viral genome sequences |
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ViTa |
microRNAs targets of the influenza virus |
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5.5. Prokaryotic genome databases |
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5.5.1. General |
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AlterORF |
Database of alternate open reading frames |
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BacMap |
Picture atlas of annotated bacterial genomes |
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Comparative Genometrics |
DNA walks, nucleotide skews and other biometric measures of prokaryotic genomes |
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EMGlib |
Enhanced microbial genomes library: Completely sequenced genomes of unicellular organisms |
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GeneDB |
Curated database for various Sanger-sequenced genomes |
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Genome Atlas |
DNA structural properties of sequenced genomes |
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HEG-DB |
Predicted highly expressed genes in prokaryotic genomes |
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HGT-DB |
Horizontal Gene Transfer-DataBase |
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IMG |
Comparative analysis of microbial genomes sequenced at the DOE Joint Genome Institute |
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IMG/M |
A data management and analysis system for metagenomes |
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Interrupted coding sequences DB |
Interrupted coding sequences: frameshifts, stop codons, sequencing errors in microbial genomes |
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MeGX |
Marine ecological genomix: genomics and metagenomics of marine bacteria |
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MetaGrowth |
Growth requirements of bacterial pathogens |
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MiST |
Microbial Signal Transduction database |
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PGTdb |
Prokaryotic growth temperature database |
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RRNDB |
rRNA operon numbers in various prokaryotes |
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Roundup |
Repository of orthologs and corresponding evolutionary distances |
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SIDDBase |
Stress-induced DNA duplex destabilization profiles of complete microbial genomes |
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xBase |
A family of group-specific bacterial genome databases, includes coliBASE, CampyDB, ClostriDB, MycoDB, PseudoDB and others |
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5.5.2. Escherichia coli |
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ASAP |
A Systematic Annotation Package |
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CCDB |
CyberCell Database |
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coliBase |
Database for E. coli,Salmonella and Shigella |
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Colibri |
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EchoBASE |
Post-genomic studies ofEscherichia coli |
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EcoCyc |
E. coli K12 genes, pathways, transporters, and gene regulation |
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EcoGene |
Sequence and literature data on E. coli genes and proteins |
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ERIC |
Enteropathogen Resource Integration Center |
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Essential genes in E. coli |
A list of genes essential for viability of E. coli |
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GenoBase |
Functional genomic aAnalysis of E. coli in Japan |
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GenProtEC |
E. coli K12 genome and proteome database |
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5.5.3. Bacillus subtilis |
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BSORF |
Bacillus subtilis Open Reading Frames |
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DBTBS |
Bacillus subtilis promoters and transcription factors |
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NRSub |
Non-redundant Bacillus subtilis database at U. Lyon |
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SubtiList |
Bacillus subtilis genome database at Institut Pasteur |
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5.5.4. Other bacteria |
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BuchneraBase |
Genomic database for the pea aphid symbiont Buchnerasp. APS |
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CampyDB |
Campylobacter Database |
Incoroporated into xBase, no. 426 |
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CIDB |
Chlamydia Interactive Database: Gene expression data |
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ClostriDB |
Clostridium Database |
Incoroporated into xBase, no. 426 |
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CoryneRegNet |
Corynebacterial transcription factors |
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CyanoBase |
Cyanobacterial genomes |
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LEGER |
Post-genome research ofListeria |
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LeptoList |
Leptospira interrogansgenome |
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MolliGen |
Genomic data on mollicutes |
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MtbRegList |
Mycobacterium tuberculosisgene regulation |
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MvirDB |
Protein toxins, virulence factors, and antibiotic resistance genes |
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PAIDB |
Pathogenicity islands in bacterial genomes |
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PATRIC |
PathoSystems Resource Integration Center |
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PEC |
Profiling of E. coliChromosome |
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PGTdb |
Prokaryotic growth temperature database |
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PseudoCAP |
Pseudomonas aeruginosacommunity genome annotation project |
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RegTransBase |
Manually curated database of regulatory interactions in prokaryotes |
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RsGDB |
Rhodobacter sphaeroidesgenome |
http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/ |
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ShiBase |
Shigella database |
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VFDB |
Virulence Factors of pathogenic bacteria |
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xanthusBase |
Genome of the social bacterium Myxococcus xanthus |
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5.5.5. Archaea |
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SulfolobusDatabase |
Comparative genomics ofSulfolobus species |
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UCSC Archaeal Genome Browser |
Pyrococcus furiosus genome browser |
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5.6. Unicellular eukaryotes genome databases |
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ApiDB |
Unified resource for various apicomplexan species |
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ApiDots |
EST sequences from variousApicomplexan parasites |
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Comparasite |
Database for comparative study of parasite cDNAs |
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CryptoDB |
Cryptosporidium database |
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Diatom EST DB |
ESTs from diatom algaeThalassiosira andPhaeodactylum |
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DictyBase |
Universal resource forDictyostelium discoideum |
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Full-Malaria |
Full-length cDNA library from erythrocytic-stagePlasmodium |
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ParameciumDB |
Paramecium genome sequencing project |
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PlasmoDB |
Plasmodium genome database |
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ProtozoaDB |
Comparative analysis of protozoan genomes |
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TBestDB |
Taxonomically broad EST database: protist ESTs |
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TcruziDB |
Trypanosoma cruzi genome database |
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ToxoDB |
Toxoplasma gondii genome database |
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U-genome |
Genome organization in unicellular eukaryotes |
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5.7. Fungi |
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CFGP |
Comparative Fungal Genomics Platform |
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Fungal Genome Size Database |
Genome sizes of various fungi |
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5.7.1. Yeasts |
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AGD |
Ashbya gossypii genome database |
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CandidaDB |
Candida albicans genome database |
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Candida Genome |
Candida albicans genome database |
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CYGD |
MIPS Comprehensive yeast genome database |
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Génolevures |
A comparison of S. cerevisiae and 14 other yeast species |
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Mpact |
Yeast protein-protein interaction data |
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PROPHECY |
Profiling of phenotypic characteristics in yeast |
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SCMD |
Saccharomyces cerevisiaemorphological database: micrographs of budding yeast mutants |
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SCPD |
Saccharomycescerevisiae promoterdatabase |
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SGD |
Saccharomyces genome database |
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TRIPLES |
Transposon-insertion phenotypes, localization, and expression inSaccharomyces |
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YDPM |
Yeast deletion project and mitochondria database |
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Yeast Intron Database |
Ares lab database of splicesomal introns in S. cerevisiae |
http://www.cse.ucsc.edu/research/compbio/yeast_ introns.html |
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YEASTRACT |
Yeast search for transcriptional regulators and consensus tracking |
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Yeast snoRNA DB |
Yeast small nucleolar RNAs |
http://www.bio.umass.edu/biochem/rna-sequence/ Yeast_snoRNA_Database/snoRNA_DataBase.html |
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YGOB |
Yeast gene order browser |
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yMGV |
Yeast microarray global viewer |
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YMPD |
Yeast mitochondrial protein database |
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YRC PDR |
Yeast resource center public data repository |
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| 5.7.2. Other fungi | ||
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CADRE |
Central Aspergillus data repository |
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COGEME |
Phytopathogenic fungi and oomycete EST database |
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FGDB |
MIPS Fusarium graminearumgenome database |
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Magnaporthe grisea DB |
Magnaporthe grisea Database |
http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/Home.html |
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MNCDB |
MIPS Neurosporacrassa database |
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OGD |
Oomycete Genomics Database: ESTs and annotation |
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PHI-base |
Genes affecting fungal pathogen-host interactions |
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PhytophthoraFunctio-nal Genomics DB |
ESTs and expression data from P. infestans and P. sojae |
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5.8. Invertebrates |
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5.8.1. Caenorhabditis elegans |
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C. elegansProject |
Genome sequencing data at the Sanger Institute |
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Intronerator |
Introns and splicing in C. elegans and C. briggsae |
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RNAiDB |
RNAi phenotypic analysis ofC. elegans genes |
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SGCEdb |
Structural genomics of C. elegans |
No longer maintained |
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WorfDB |
C. elegans ORFeome |
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WormBase |
Data repository for C. elegans and C. briggsae:curated genome annotation, genetic and physical maps, pathways |
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WormBook |
Peer-reviewed chapters on the biology of C. elegans |
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5.8.2. Drosophila melanogaster |
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DPDB |
Drosophila polymorphism database |
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DroID |
Drosophila gene and protein interaction data |
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Drosophilamicroarray centre |
Canadian Drosophilamicroarray centre |
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DroSpeGe |
Drosophila Species Genomes |
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FLIGHT |
Drosophila phenotypes, gene expression and protein interactions |
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FlyBase |
Drosophila sequences and genomic information |
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FlyBrain |
Database of the Drosophilanervous system |
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FlyMine |
Integration of insect genomic and proteomic data |
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FlyRNAi DRSC |
Genome-wide RNAi analysis data in Drosophila |
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FLYSNP |
Single nucleotide polymorphism data forDrosophilamelanogaster |
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FlyTF |
Drosophila Transcription Factors |
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FlyTrap |
Drosophila mutants created using protein trap strategy |
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FlyView |
Drosophila development and genetics |
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GadFly |
Genome annotation database of Drosophila |
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GeniSys |
Enhancer- and promoter-inserted mutants ofDrosophila |
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GenomeRNAi |
Cell-based RNAi phenotypes database |
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Homophila |
Drosophila homologs of human disease genes |
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InterActive Fly |
Drosophila genes and their roles in development |
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REDfly |
Regulatory modules and transcription factor binding sites in Drosophila |
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5.8.3. Other invertebrates |
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ACeDB |
C. elegans, S. pombe, and human genomic information |
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AphidBase |
Genomic database for the pea aphid (Acyrthosiphon pisum) |
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AppaDB |
Database on the nematodePristionchus pacificus |
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BeetleBase |
Genome database of the beetle Tribolium castaneum |
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ButterflyBase |
Genomics of butterflies (Lepidoptera) |
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Ciliate IES-MDS Db |
Macro- and micronuclear genes in spirotrichous ciliates |
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CnidBase |
Cnidarian evolution and gene expression database |
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CuticleDB |
Structural proteins of Arthropod cuticle |
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LumbriBASE |
ESTs of the earthwormLumbricus rubellus |
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Nematode.net |
Parasitic nematode sequencing project |
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NEMBASE |
Nematode sequence and functional data database |
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PPNEMA |
Plant-parasitic nematode rRNAs |
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Pristionchus.org |
Genome data of the nematode <I>Pristionchus pacificus</I> |
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Sebida |
Sex bias in insect gene expression database |
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SilkDB |
Silkworm Bombyx mori ESTs, mutants, photographs |
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SilkSatDb |
A microsatellite database of the silkworm Bombyx mori |
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SmedGD |
The Schmidtea mediterraneagenome database |
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SpodoBase |
Genomics of the butterflySpodoptera frugiperda |
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StellaBase |
Nematostella vectensis (sea anemone) genome |
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TetrahymenaGenome DB |
Tetrahymena thermophilagenome database |
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VectorBase |
Invertebrate Vectors of Human Pathogens |
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wFleaBase |
Daphnia Water Flea Genome Database |
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