GenBank

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GenBank
Content
Description Nucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation.
Data types captured
  • Nucleotide sequence
  • Protein sequence
Organisms all
Contact
Research center NCBI
Primary citation PMID 21071399
Release date 1982; 31 years ago (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.

Contents

Submissions [edit]

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 [edit]

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]

Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.

Growth [edit]

Growth in GenBank base pairs, 1982 to 2007, on a semi-log scale

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 (2013-02-15), 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.

Top organisms in GenBank (Release 179)[7]
Organism base pairs
Homo sapiens 701014792487417000014,792,487,417
Mus musculus 70098859010528000008,859,010,528
Rattus norvegicus 70096443768086000006,443,768,086
Bos taurus 70095361712195000005,361,712,195
Zea mays 70095037629354000005,037,629,354
Sus scrofa 70094783381701000004,783,381,701
Danio rerio 70093137945523000003,137,945,523
Strongylocentrotus purpuratus 70091352920226000001,352,920,226
Oryza sativa Japonica Group 70091197245122000001,197,245,122
Nicotiana tabacum 70091187388273000001,187,388,273
Xenopus (Silurana) tropicalis 70091147132278000001,147,132,278
Drosophila melanogaster 70091047707620000001,047,707,620
Pan troglodytes 70091001926471000001,001,926,471
Arabidopsis thaliana 70091001073627000001,001,073,627
Canis lupus familiaris 7008943043649000000943,043,649
Vitis vinifera 7008913911649000000913,911,649
Gallus gallus 7008891463513000000891,463,513
Glycine max 7008886103518000000886,103,518
Macaca mulatta 7008821393285000000821,393,285
Ciona intestinalis 7008748350657000000748,350,657

See also [edit]

References [edit]

  1. ^ Benson D, et al.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L. (2008). "GenBank". Nucleic Acids Research 36 (Database): D25–D30. doi:10.1093/nar/gkm929. PMC 2238942. PMID 18073190. 
  2. ^ Benson D, et al.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2009). "GenBank". Nucleic Acids Research 37 (Database): D26–D31. doi:10.1093/nar/gkn723. PMC 2686462. PMID 18940867. 
  3. ^ a b c "GenBank release notes". NCBI. 
  4. ^ Hanson, Todd (2000-11-21). "Walter Goad, GenBank founder, dies". Newsbulletin: obituary. Los Alamos National Laboratory. 
  5. ^ LANL GenBank History
  6. ^ 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. 
  7. ^ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW (January 2011). "GenBank". Nucleic Acids Res. 39 (Database issue): D32–37. doi:10.1093/nar/gkq1079. PMC 3013681. PMID 21071399. 


External links [edit]
Databases
Other
Institutions
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