Template:Short description Template:Infobox biodatabase The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International 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 described species.<ref>Template:Cite journal</ref><ref name=":0">Template:Cite journal</ref>
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.<ref name="pmid18073190">Template:Cite journal</ref><ref name="pmid18940867">Template:Cite journal</ref><ref name=":0" />
GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.
SubmissionsEdit
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 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.<ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref><ref>{{#invoke:citation/CS1|citation |CitationClass=web }}</ref>
HistoryEdit
Walter Goad of the Theoretical Biology and Biophysics Group at Los 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.<ref name="lanl2000">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref> 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.<ref name="lanl1994">LANL GenBank History</ref> 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).<ref name="pmid2326192">Template:Cite journal</ref>
GrowthEdit
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".<ref name="ReleaseNotes">{{#invoke:citation/CS1|citation |CitationClass=web }}</ref><ref>Template:Cite journal</ref> As of 15 June 2022, GenBank release 250.0 has over 239 million loci, 1,39 trillion nucleotide bases, from 239 million reported sequences.<ref name="ReleaseNotes" />
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 | Template:Nts |
| SARS-CoV-2 | Template:Nts |
| Hordeum vulgare subsp. vulgare | Template:Nts |
| Mus musculus | Template:Nts |
| Homo sapiens | Template:Nts |
| Avena sativa | Template:Nts |
| Escherichia coli | Template:Nts |
| Klebsiella pneumoniae | Template:Nts |
| Danio rerio | Template:Nts |
| Bos taurus | Template:Nts |
| Triticum turgidum subsp. durum | Template:Nts |
| Zea mays | Template:Nts |
| Avena insularis | Template:Nts |
| Secale cereale | Template:Nts |
| Rattus norvegicus | Template:Nts |
| Aegilops longissima | Template:Nts |
| Canis lupus familiaris | Template:Nts |
| Aegilops sharonensis | Template:Nts |
| Sus scrofa | Template:Nts |
| Rhinatrema bivittatum | Template:Nts |
LimitationsEdit
An analysis of Genbank and other services for the molecular identification of clinical blood culture isolates using 16S rRNA sequences<ref>Template:Cite journal</ref> showed that such analyses were more discriminative when GenBank was combined with other services such as EzTaxon-e<ref>EzTaxon-e Database eztaxon-e.ezbiocloud.net (archive accessed 25 March 2021)</ref> and the BIBI<ref>leBIBI V5 pbil.univ-lyon1.fr (archive accessed 25 March 2021)</ref> 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 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.<ref>Template:Cite journal</ref> 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.<ref name="van den BurgHerrando-PérezVieites2020">Template:Cite journal</ref><ref name="LiShenChen2018">Template:Cite journal</ref><ref name="HellerCasalettoRuiz2018">Template:Cite journal</ref> 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.<ref name="Van Den BurgVieites2022">Template:Cite journal</ref>
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.<ref>Template:Cite journal</ref>
See alsoEdit
- Ensembl
- Human Protein Reference Database (HPRD)
- Sequence analysis
- UniProt
- List of sequenced eukaryotic genomes
- List of sequenced archaeal genomes
- RefSeq — the Reference Sequence Database
- Geneious — includes a GenBank Submission Tool
- Open science data
- Open Standard
ReferencesEdit
- {{#invoke:template wrapper|wrap|_template=Include-USGov
|agency=National Center for Biotechnology Information |url=https://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook.TOC&depth=2 |article=NCBI Handbook |work={{#if:|NCBI Handbook}}}}
External linksEdit
- 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?