Editing GenBank

{{short description|DNA sequence database}}
{{infobox biodatabase
| title       = GenBank
| author      =
| center      = [[National Center for Biotechnology Information|NCBI]]
| organism    = All
| released    = {{Start date and age|1982}}
| description = Nucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation.
| scope       = {{ubl|Nucleotide sequence|Protein sequence}}
| url         = [https://www.ncbi.nlm.nih.gov/ NCBI]
| download    = [http://ftp.ncbi.nih.gov/ ncbi ftp]
| webservice  = {{ubl | [http://eutils.ncbi.nlm.nih.gov/ eutils] | [http://eutils.ncbi.nlm.nih.gov/soap/v2.0/eutils.wsdl soap]}}
| license     = Unclear<ref>The [http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/ download page] at [[University of California, Santa Cruz|UCSC]] says "[[National Center for Biotechnology Information|NCBI]] places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim [[Biological patent|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."</ref>
| webapp      = [[BLAST (biotechnology)|BLAST]]
| standalone  = BLAST
| format      = {{Plainlist|
* [[XML]]
* [[ASN.1]]
* Genbank format
}}
| pmid        =  21071399
}}
The '''GenBank''' [[sequence database]] is an [[Open access (publishing)|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>{{Cite journal |author=Eric W Sayers |author2=Mark Cavanaugh |author3=Karen Clark |author4=Kim D Pruitt |author5=Conrad L Schoch |author6=Stephen T Sherry |author7=Ilene Karsch-Mizrachi |date=7 January 2022 |title=GenBank |journal=Nucleic Acids Archive |volume=50 |issue=D1 |pages=D161–D164 |doi=10.1093/nar/gkab1135 |doi-access=free|pmid=34850943 |pmc=8690257 }}</ref><ref name=":0">{{Cite journal |last1=Sayers |first1=Eric W |last2=Cavanaugh |first2=Mark |last3=Frisse |first3=Linda |last4=Pruitt |first4=Kim D |last5=Schneider |first5=Valerie A |last6=Underwood |first6=Beverly A |last7=Yankie |first7=Linda |last8=Karsch-Mizrachi |first8=Ilene |date=2025-01-06 |title=GenBank 2025 update |url=https://academic.oup.com/nar/article/53/D1/D56/7903376 |journal=Nucleic Acids Research |volume=53 |issue=D1 |pages=D56–D61 |doi=10.1093/nar/gkae1114 |issn=0305-1048 |pmc=11701615 |pmid=39558184}}</ref>

The database started in 1982 by [[Walter Goad]] and [[LANL|Los Alamos National Laboratory]]. GenBank has become an important database for research in biological fields and has grown in recent years at an [[Exponential growth|exponential rate]] by doubling roughly every 18 months.<ref name="pmid18073190">{{cite journal | author=Benson D | title=GenBank | journal=Nucleic Acids Research | year=2008 | volume=36 | issue=Database | pages=D25–D30 | doi=10.1093/nar/gkm929 | pmid=18073190 | pmc=2238942 | last2=Karsch-Mizrachi | first2=I. | last3=Lipman | first3=D. J. | last4=Ostell | first4=J. | last5=Wheeler | first5=D. L. |display-authors=etal}}</ref><ref name="pmid18940867">{{cite journal | author=Benson D | title=GenBank | journal=Nucleic Acids Research | year=2009 | volume=37 | issue=Database | pages=D26–D31 | doi=10.1093/nar/gkn723 | pmid=18940867 | pmc=2686462 | last2=Karsch-Mizrachi | first2=I. | last3=Lipman | first3=D. J. | last4=Ostell | first4=J. | last5=Sayers | first5=E. W. |display-authors=etal}}</ref><ref name=":0" />

GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale [[DNA sequencing|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, table2asn. Upon receipt of a sequence submission, the GenBank staff examines the originality of the data and assigns an [[Accession number (bioinformatics)|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 [[File Transfer Protocol|FTP]]. Bulk submissions of [[Expressed Sequence Tag]] (EST), [[Sequence-tagged site]] (STS), [[Genome survey sequence|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>{{Cite web |title=How to submit data to GenBank |url=https://www.ncbi.nlm.nih.gov/genbank/submit/ |access-date=20 July 2022 |website=NCBI}}</ref><ref>{{Cite web |title=GenBank Submission Types |url=https://www.ncbi.nlm.nih.gov/genbank/submit_types/ |access-date=20 July 2022 |website=NCBI}}</ref>

== History ==
[[Walter Goad]] of the Theoretical Biology and Biophysics Group at [[LANL|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">{{cite web |last=Hanson |first=Todd |title=Walter Goad, GenBank founder, dies |work=Newsbulletin: obituary |publisher=Los Alamos National Laboratory |date=2000-11-21 |url=http://www.lanl.gov/orgs/pa/News/112100.html}}</ref> Funding was provided by the [[National Institutes of Health]], the [[National Science Foundation]], the [[United States Department of Energy|Department of Energy]], and the [[United States Department of Defense|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">[http://www.bio.net/bionet/mm/bionews/1994-January/000877.html 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 (publishing)|open access]] communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created [[National Center for Biotechnology Information|National Center for Biotechnology Information (NCBI)]].<ref name="pmid2326192">{{cite journal | author=Benton D | title=Recent changes in the GenBank On-line Service | journal=Nucleic Acids Research | year=1990 | volume=18 | issue=6 | pages= 1517–1520 | doi=10.1093/nar/18.6.1517 | pmid=2326192 | pmc=330520}}</ref>

[[File:NucleotideSequences 86 87.jpeg|300px|thumb|Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.]]

[[File:Genbank100CD.jpg|300px|thumb|CD-ROM of Genbank v100]]

==Growth==
[[Image:Growth of Genbank.svg|thumb|Growth in GenBank base pairs, 1982 to 2018, on a [[semilog graph|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".<ref name="ReleaseNotes">{{cite web |date=15 June 2022 |title=GenBank release notes (Release 250) |url=http://ftp.ncbi.nih.gov/genbank/gbrel.txt |access-date=20 July 2022 |publisher=NCBI}}</ref><ref>{{Cite journal 
| last1 = Benson | first1 = D. A. 
| last2 = Cavanaugh | first2 = M. 
| last3 = Clark | first3 = K. 
| last4 = Karsch-Mizrachi | first4 = I. 
| last5 = Lipman | first5 = D. J. 
| last6 = Ostell | first6 = J. 
| last7 = Sayers | first7 = E. W. 
| doi = 10.1093/nar/gks1195 
| title = GenBank 
| journal = Nucleic Acids Research 
| volume = 41 
| issue = Database issue 
| pages = D36–D42 
| year = 2012 
| pmid = 23193287 
| pmc =3531190 
}}</ref> As of 15 June 2022, GenBank release 250.0 has over 239 million [[Locus (genetics)|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. 
{| class="wikitable sortable"
|+Top 20 organisms in GenBank (Release 250)<ref name="ReleaseNotes" />
! Organism
! [[base pairs]]
|- 
| ''[[Common wheat|Triticum aestivum]]''
| align="middle" | {{Nts|215443744183}}
|-
|[[SARS-CoV-2]]
| align="middle" | {{Nts|165771825746}}
|-
|''[[Barley|Hordeum vulgare]]'' subsp. ''vulgare''
| align="middle" | {{Nts|101344340096}}
|- 
| ''[[House mouse|Mus musculus]]''
| align="middle" | {{nts|30614386913}}
|- 
| ''[[Human|Homo sapiens]]''
| align="middle" | {{nts|27834633853}}
|-
|''[[Oat|Avena sativa]]''
| align="middle" | {{Nts|21127939362}}
|-
|''[[Escherichia coli]]''
| align="middle" | {{Nts|15517830491}}
|-
|''[[Klebsiella pneumoniae]]''
| align="middle" | {{Nts|11144687122}}
|- 
| ''[[Zebrafish|Danio rerio]]''
| align="middle" | {{nts|10890148966}}
|- 
| ''[[Cattle|Bos taurus]]''
| align="middle" | {{nts|10650671156}}
|-
|''[[Durum|Triticum turgidum]]'' subsp. ''durum''
| align="middle" | {{Nts|9981529154}}
|- 
| ''[[Maize|Zea mays]]''
| align="middle" | {{nts|7412263902}}
|-
|''[[Avena insularis]]''
| align="middle" | {{Nts|6924307246}}
|-
|''[[Rye|Secale cereale]]''
| align="middle" | {{Nts|6749247504}}
|- 
| ''[[Brown rat|Rattus norvegicus]]''
| align="middle" | {{nts|6548854408}}
|-
|''[[Aegilops longissima]]''
| align="middle" | {{Nts|5920483689}}
|- 
| ''[[Dog|Canis lupus familiaris]]''
| align="middle" | {{nts|5776499164}}
|-
|''[[Aegilops sharonensis]]''
| align="middle" | {{Nts|5272476906}}
|- 
| ''[[Wild boar|Sus scrofa]]''
| align="middle" | {{nts|5179074907}}
|-
|''[[Rhinatrema bivittatum]]''
| align="middle" | {{Nts|5178626132}}
|}

==Limitations==
An analysis of Genbank and other services for the molecular identification of clinical blood culture isolates using [[16S ribosomal RNA|16S rRNA]] sequences<ref>{{cite journal |author=Kyung Sun Park |author2=Chang-Seok Ki |author3=Cheol-In Kang |author4=Yae-Jean Kim |author5=Doo Ryeon Chung |author6=Kyong Ran Peck |author7=Jae-Hoon Song |author8=Nam Yong Lee |journal= J. Clin. Microbiol.|date= May 2012|volume=50|number= 5 |pages=1792–1795|title= Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods|doi=10.1128/JCM.00081-12|pmid= 22403421|pmc=3347139}}</ref> showed that such analyses were more discriminative when GenBank was combined with other services such as [[EzTaxon Database|EzTaxon]]-e<ref>[https://web.archive.org/web/20130928154318/http://eztaxon-e.ezbiocloud.net/ EzTaxon-e Database] ''eztaxon-e.ezbiocloud.net'' (archive accessed 25 March 2021)</ref> and the BIBI<ref>[https://web.archive.org/web/20151001000357/http://pbil.univ-lyon1.fr/bibi/ 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>{{Cite journal|last1=Ogwang|first1=Joel|last2=Bariche|first2=Michel|last3=Bos|first3=Arthur R.|date=2021|title=Genetic diversity and phylogenetic relationships of threadfin breams (''Nemipterus'' spp.) from the Red Sea and eastern Mediterranean Sea|url=https://cdnsciencepub.com/doi/full/10.1139/gen-2019-0163|journal=Genome|language=en|volume=64|issue=3|pages=207–216|doi=10.1139/gen-2019-0163|pmid=32678985 |url-access=subscription}}</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">{{cite journal | last1 = van den Burg | first1 = Matthijs P. | last2 = Herrando-Pérez | first2 = Salvador | last3 = Vieites | first3 = David R. | title = ACDC, a global database of amphibian cytochrome-b sequences using reproducible curation for GenBank records | journal = Scientific Data | date = 13 August 2020 | volume = 7 | issue = 1 | page = 268 | eissn = 2052-4463 | doi = 10.1038/s41597-020-00598-9 | pmid = 32792559 | pmc = 7426930 | bibcode = 2020NatSD...7..268V | url = }}</ref><ref name="LiShenChen2018">{{cite journal | last1 = Li | first1 = Xiaobing | last2 = Shen | first2 = Xuejuan | last3 = Chen | first3 = Xiao | last4 = Xiang | first4 = Dan | last5 = Murphy | first5 = Robert W. | last6 = Shen | first6 = Yongyi | title = Detection of Potential Problematic Cytb Gene Sequences of Fishes in GenBank | journal = Frontiers in Genetics | date = 6 February 2018 | volume = 9 | page = 30 | eissn = 1664-8021 | doi = 10.3389/fgene.2018.00030 | pmid = 29467794 | pmc = 5808227 | url =  | doi-access = free }}</ref><ref name="HellerCasalettoRuiz2018">{{cite journal | last1 = Heller | first1 = Philip | last2 = Casaletto | first2 = James | last3 = Ruiz | first3 = Gregory | last4 = Geller | first4 = Jonathan | title = A database of metazoan cytochrome c oxidase subunit I gene sequences derived from GenBank with CO-ARBitrator | journal = Scientific Data | date = 7 August 2018 | volume = 5 | issue = 1 | eissn = 2052-4463 | doi = 10.1038/sdata.2018.156 | pmid = 30084847 | pmc = 6080493 | bibcode = 2018NatSD...580156H | url = }}</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">{{cite journal | last1 = Van Den Burg | first1 = Matthijs P. | last2 = Vieites | first2 = David R. | title = <nowiki>Bird genetic databases need improved curation and error reporting to            <scp>NCBI</scp></nowiki> | journal = Ibis | date = 22 September 2022 | issn = 0019-1019 | eissn = 1474-919X | doi = 10.1111/ibi.13143 | pmid = | url = | doi-access = free | hdl = 10261/282622 | hdl-access = free }}</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>{{Cite journal |last1=Garg |first1=Akhil |last2=Leipe |first2=Detlef |last3=Uetz |first3=Peter |date=2019-12-10 |title=The disconnect between DNA and species names: lessons from reptile species in the NCBI taxonomy database |url=https://www.mapress.com/zt/article/view/zootaxa.4706.3.1 |journal=Zootaxa |language=en |volume=4706 |issue=3 |pages=401–407 |doi=10.11646/zootaxa.4706.3.1 |issn=1175-5334}}</ref>

==See also==

* [[Ensembl]]
* [[Human Protein Reference Database]] (HPRD)
* [[Sequence analysis]]
* [[UniProt]]
* [[List of sequenced eukaryotic genomes]]
* [[List of sequenced archaeal genomes]]
* [[RefSeq]] &mdash; the Reference Sequence Database
* [[Geneious]] &mdash; includes a GenBank Submission Tool
* [[Open science data]]
*[[Open Standard]]

== References ==
{{reflist|30em}}

*{{NCBI-handbook}}

==External links==
*[https://www.ncbi.nlm.nih.gov/sites/entrez?db=nucleotide GenBank]
*[https://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=28302128 Example sequence record, for hemoglobin beta]
*[https://www.ncbi.nlm.nih.gov/BankIt/ BankIt]
*[https://www.ncbi.nlm.nih.gov/Sequin/index.html Sequin] &mdash; a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.
*[http://emboss.sourceforge.net EMBOSS] &mdash; free, open source software for molecular biology
*[https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=handbook.section.GenBank_ASM GenBank, RefSeq, TPA and UniProt: What's in a Name?]

{{Bioinformatics}}

{{Authority control}}

[[Category:National Institutes of Health]]
[[Category:Genetics databases]]
[[Category:Genome databases]]
[[Category:Bioinformatics]]
[[Category:Biological databases]]