GenBank
| Content | |
|---|---|
| Description | Nucleotide sequences for more than 300 000 organisms with supporting bibliographic and biological annotation. |
| Data types captured | Nucleotide Sequence, Protein sequence |
| Organism(s) | all |
| Contact | |
| Research center | NCBI |
| Primary Citation | PMID 21071399 |
| Release date | 1982 |
| Access | |
| Data format | XML ASN.1 Genbank format |
| Website | NCBI |
| Download URL | ncbi ftp |
| Web Service URL | eutils soap |
| 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 more than 20 years since its establishment, GenBank has become the most important and most influential database for research in almost all biological fields, whose data were 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 155, produced in August 2006, contained over 65 billion nucleotide bases in more than 61 million sequences.[3] GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
Contents |
[edit] 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.
[edit] 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]
[edit] 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".[7] The following plot clearly shows the exponential growth (on a semi-log scale such as this, a straight line represents an exponential change).
As of 15 December 2011[update], GenBank release 187.0 has 146,413,798 loci, 135,117,731,375 bases, from 146,413,798 reported sequences.[7]
The GenBank database includes additional data sets which are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.
[edit] See also
- Ensembl
- HPRD
- Sequence analysis
- Sequence profiling tool
- Sequence motif
- UniProt
- List of sequenced eukaryotic genomes
- List of sequenced archeal genomes
- RefSeq - the Reference Sequence Database
[edit] References
- ^ Benson, D. et al. (2008). "GenBank". Nucleic Acids Research 36 (Database): D25–D30. doi:10.1093/nar/gkm929. PMC 2238942. PMID 18073190. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2238942.
- ^ Benson, D. et al. (2009). "GenBank". Nucleic Acids Research 37 (Database): D26–D31. doi:10.1093/nar/gkn723. PMC 2686462. PMID 18940867. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2686462.
- ^ Benson, D. et al. (2006). "GenBank". Nucleic Acids Research 34 (Database): D16–D20. doi:10.1093/nar/gkj157. PMC 1347519. PMID 16381837. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1347519.
- ^ Hanson, Todd (2000-11-21). "Walter Goad, GenBank founder, dies". Newsbulletin: obituary. Los Alamos National Laboratory. http://www.lanl.gov/orgs/pa/News/112100.html.
- ^ 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. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=330520.
- ^ a b "GenBank release notes". NCBI. ftp://ftp.ncbi.nih.gov/genbank/gbrel.txt.
This article incorporates public domain material from the National Center for Biotechnology Information document "NCBI Handbook".
This article incorporates 
