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GenBank
Content
Description
Nucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation.
GenBank and its collaborators will receive sequences produced in laboratories throughout the world from more than 500,000 formally described species.[2] The database started in 1982 by Walter Goad and Los Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months.[3][4]
Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences.[5] 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.[6][7]
In the mid-1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL.[9] 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 (NCBI).[10]
Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.CD-ROM of Genbank v100
Growth
Growth in GenBank base pairs, 1982 to 2018, on a semi-log scale
The GenBank release 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".[5][11] As of 15 June 2022, GenBank release 250.0 has over 239 million loci, 1,39 trillion nucleotide bases, from 239 million reported sequences.[5]
The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.
Public databases which may be searched using the National Center for Biotechnology Information Basic Local Alignment Search Tool (NCBI BLAST), lack peer-reviewed sequences of type strains and sequences of non-type strains. On the other hand, while commercial databases potentially contain high-quality filtered sequence data, there are a limited number of reference sequences.
A paper released in the Journal of Clinical Microbiology[12] evaluated the 16S rRNA gene sequencing results analyzed with GenBank in conjunction with other freely available, quality-controlled, web-based public databases, such as the EzTaxon-e[13] and the BIBI[14] databases. The results showed that analyses performed using GenBank combined with EzTaxon-e (kappa = 0.79) were more discriminative than using GenBank (kappa = 0.66) or other databases alone.
GenBank, being a public database, may contain sequences wrongly assigned to a particular species, because the initial identification of the organism was wrong. A recent article published in Genome showed that 75% of mitochondrial Cytochrome c oxidase subunit I sequences were wrongly assigned to the fish Nemipterus mesoprion resulting from continued usage of sequences of initially misidentified individuals.[15] 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.[16][17][18]
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 all Cytochrome b records of birds further showed that 45% of the identified erroneous records lack a voucher specimen that prevents a reassessment of the species identification.[19]
^The download page at UCSC says "NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NCBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in GenBank."
^Eric W Sayers; Mark Cavanaugh; Karen Clark; Kim D Pruitt; Conrad L Schoch; Stephen T Sherry; Ilene Karsch-Mizrachi (7 January 2022). "GenBank". Nucleic Acids Archive. 50 (D1): D161–D164. doi:10.1093/nar/gkab1135. PMC8690257. PMID34850943.
