| 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; 43 years ago (1982) |
| Access | |
| Data format | |
| Website | NCBI |
| Download URL | ncbi ftp |
| Web service URL | |
| Tools | |
| Web | BLAST |
| Standalone | BLAST |
| Miscellaneous | |
| License | Unclear[1] |
TheGenBanksequence database is anopen access, annotated collection of all publicly availablenucleotide sequences and theirprotein translations. It is produced and maintained by theNational Center for Biotechnology Information (NCBI; a part of theNational Institutes of Health in theUnited States) as part of theInternational Nucleotide Sequence Database Collaboration (INSDC).
In October 2024, GenBank contained 34 trillion base pairs from over 4.7 billion nucleotide sequences and more than 580,000 formally describedspecies.[2][3]
The database started in 1982 byWalter Goad andLos Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at anexponential rate by doubling roughly every 18 months.[4][5][3]
GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scalesequencing centers.
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, table2asn. Upon receipt of a sequence submission, the GenBank staff examines the originality of the data and assigns anaccession number to the sequence and performs quality assurance checks. The submissions are then released to the public database, where the entries are retrievable byEntrez or downloadable byFTP. Bulk submissions ofExpressed Sequence Tag (EST),Sequence-tagged site (STS),Genome Survey Sequence (GSS), andHigh-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.[6][7]
Walter Goad of the Theoretical Biology and Biophysics Group atLos Alamos National Laboratory (LANL) and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank.[8] Funding was provided by theNational Institutes of Health, theNational Science Foundation, theDepartment of Energy, and theDepartment of Defense. LANL collaborated on GenBank with the firmBolt, 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 atStanford University managed the GenBank project in collaboration with LANL.[9] As one of the earliestbioinformatics community projects on the Internet, the GenBank project startedBIOSCI/Bionet news groups for promotingopen access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly createdNational Center for Biotechnology Information (NCBI).[10]
The GenBankrelease notes for release 250.0 (June 2022) state that "from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months".[11][12] As of 15 June 2022, GenBank release 250.0 has over 239 millionloci, 1,39 trillion nucleotide bases, from 239 million reported sequences.[11]
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 |
|---|---|
| Triticum aestivum | 2.15443744183×10 |
| SARS-CoV-2 | 1.65771825746×10 |
| Hordeum vulgare subsp.vulgare | 1.01344340096×10 |
| Mus musculus | 3.0614386913×10 |
| Homo sapiens | 2.7834633853×10 |
| Avena sativa | 2.1127939362×10 |
| Escherichia coli | 1.5517830491×10 |
| Klebsiella pneumoniae | 1.1144687122×10 |
| Danio rerio | 1.0890148966×10 |
| Bos taurus | 1.0650671156×10 |
| Triticum turgidum subsp.durum | 9.981529154×10 |
| Zea mays | 7.412263902×10 |
| Avena insularis | 6.924307246×10 |
| Secale cereale | 6.749247504×10 |
| Rattus norvegicus | 6.548854408×10 |
| Aegilops longissima | 5.920483689×10 |
| Canis lupus familiaris | 5.776499164×10 |
| Aegilops sharonensis | 5.272476906×10 |
| Sus scrofa | 5.179074907×10 |
| Rhinatrema bivittatum | 5.178626132×10 |
An analysis of Genbank and other services for the molecular identification of clinical blood culture isolates using16S rRNA sequences[13] showed that such analyses were more discriminative when GenBank was combined with other services such asEzTaxon-e[14] and the BIBI[15] databases.
GenBank may contain sequences wrongly assigned to a particular species, because the initial identification of the organism was wrong. A recent study showed that 75% of mitochondrialCytochrome c oxidase subunit I sequences were wrongly assigned to the fishNemipterus mesoprion resulting from continued usage of sequences of initially misidentified individuals.[16] The authors provide recommendations how to avoid further distribution of publicly available sequences with incorrect scientific names.
Numerous published manuscripts have identified erroneous sequences on GenBank.[17][18][19] These are not only incorrect species assignments (which can have different causes) but also include chimeras and accession records with sequencing errors. A recent manuscript on the quality of allCytochrome b records ofbirds further showed that 45% of the identified erroneous records lack a voucher specimen that prevents a reassessment of the species identification.[20]
Another problem is that sequence records are often submitted as anonymous sequences without species names (e.g. as "Pelomedusa sp. A CK-2014" because the species are either unknown or withheld for publication purposes. However, even after the species have been identified or published, these sequence records are not updated and thus may cause ongoing confusion.[21]
This article incorporatespublic domain material fromNCBI Handbook.National Center for Biotechnology Information.| International | |
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