GenBank
| Content | |
|---|---|
| Description | Nucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation. |
| Data types captured |
|
| Organisms | all |
| Contact | |
| Research center | NCBI |
| Primary citation | PMID 21071399 |
| Release date | 1982 |
| Access | |
| Data format | |
| Website | NCBI |
| Download URL | ncbi ftp |
| Web service URL | |
| Tools | |
| Web | BLAST |
| Standalone | BLAST |
| Miscellaneous | |
| License | Public domain-US Government |
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration (INSDC). The National Center for Biotechnology Information is a part of the National Institutes of Health in the United States. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. In the more than 30 years since its establishment, GenBank has become the most important and most influential database for research in almost all biological fields, whose data are accessed and cited by millions of researchers around the world. GenBank continues to grow at an exponential rate, doubling every 18 months.[1][2] Release 194, produced in February 2013, contained over 150 billion nucleotide bases in more than 162 million sequences.[3] GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
Submissions
Only original sequences can be submitted to GenBank. Direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a sequence submission, the GenBank staff examines the originality of the data and assigns an accession number to the sequence and performs quality assurance checks. The submissions are then released to the public database, where the entries are retrievable by Entrez or downloadable by FTP. Bulk submissions of Expressed Sequence Tag (EST), Sequence-tagged site (STS), Genome Survey Sequence (GSS), and High-Throughput Genome Sequence (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences.
History
Walter Goad of the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank.[4] Funding was provided by the National Institutes of Health, the National Science Foundation, the Department of Energy, and the Department of Defense. LANL collaborated on GenBank with the firm Bolt, Beranek, and Newman, and by the end of 1983 more than 2,000 sequences were stored in it.
In the mid 1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL.[5] As one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information.[6]
Growth
The GenBank release notes for release 162.0 (October 2007) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months".[3]
As of 15 February 2013[update], GenBank release 194.0 has 162,886,727 loci, 150,141,354,858 bases, from 162,886,727 reported sequences.[3]
The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.
| Organism | base pairs |
|---|---|
| Homo sapiens | 1.4792487417×1010 |
| Mus musculus | 8.859010528×109 |
| Rattus norvegicus | 6.443768086×109 |
| Bos taurus | 5.361712195×109 |
| Zea mays | 5.037629354×109 |
| Sus scrofa | 4.783381701×109 |
| Danio rerio | 3.137945523×109 |
| Strongylocentrotus purpuratus | 1.352920226×109 |
| Oryza sativa Japonica Group | 1.197245122×109 |
| Nicotiana tabacum | 1.187388273×109 |
| Xenopus (Silurana) tropicalis | 1.147132278×109 |
| Drosophila melanogaster | 1.04770762×109 |
| Pan troglodytes | 1.001926471×109 |
| Arabidopsis thaliana | 1.001073627×109 |
| Canis lupus familiaris | 943,043,649 |
| Vitis vinifera | 913,911,649 |
| Gallus gallus | 891,463,513 |
| Glycine max | 886,103,518 |
| Macaca mulatta | 821,393,285 |
| Ciona intestinalis | 748,350,657 |
See also
- Ensembl
- Human Protein Reference Database (HPRD)
- Sequence analysis
- UniProt
- List of sequenced eukaryotic genomes
- List of sequenced archeal genomes
- RefSeq — the Reference Sequence Database
References
- ^ Benson D; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L.; et al. (2008). "GenBank". Nucleic Acids Research. 36 (Database): D25–D30. doi:10.1093/nar/gkm929. PMC 2238942. PMID 18073190.
{{cite journal}}: Explicit use of et al. in:|author=(help) - ^ Benson D; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W.; et al. (2009). "GenBank". Nucleic Acids Research. 37 (Database): D26–D31. doi:10.1093/nar/gkn723. PMC 2686462. PMID 18940867.
{{cite journal}}: Explicit use of et al. in:|author=(help) - ^ a b c "GenBank release notes". NCBI.
- ^ Hanson, Todd (2000-11-21). "Walter Goad, GenBank founder, dies". Newsbulletin: obituary. Los Alamos National Laboratory.
- ^ LANL GenBank History
- ^ Benton D (1990). "Recent changes in the GenBank On-line Service". Nucleic Acids Research. 18 (6): 1517–1520. doi:10.1093/nar/18.6.1517. PMC 330520. PMID 2326192.
- ^ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (2011). "GenBank". Nucleic Acids Res. 39 (Database issue): D32–37. doi:10.1093/nar/gkq1079. PMC 3013681. PMID 21071399.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates public domain material from NCBI Handbook. National Center for Biotechnology Information.
External links
- GenBank
- Example sequence record, for hemoglobin beta
- BankIt
- Sequin — a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.
- EMBOSS — free, open source software for molecular biology
- GenBank, RefSeq, TPA and UniProt: What's in a Name?
- GenBank File-Format Converter
