GenBank

The GenBank sequence database is an open access, annotated

collection of all publicly available nucleotide sequences and their
GenBank
protein translations. It is produced and maintained by the National Content
Center for Biotechnology Information (NCBI; a part of the Description Nucleotide
National Institutes of Health in the United States) as part of the
sequences for
International Nucleotide Sequence Database Collaboration
more than
(INSDC).
300,000
GenBank and its collaborators receive sequences produced in organisms with
laboratories throughout the world from more than 500,000 supporting
formally described species.[2] The database started in 1982 by bibliographic
Walter Goad and Los Alamos National Laboratory. GenBank has and biological
become an important database for research in biological fields and annotation.
has grown in recent years at an exponential rate by doubling
Data types Nucleotide
roughly every 18 months.[3][4]
captured sequence
Release 250.0, published in June 2022, contained over 17 trillion Protein
nucleotide bases in more than 2,45 billion sequences.[5] GenBank sequence
is built by direct submissions from individual laboratories, as well
as from bulk submissions from large-scale sequencing centers. Organisms All
Contact
Submissions Research center NCBI
Primary citation PMID 21071399
Only original sequences can be submitted to GenBank. Direct (https://pubme
submissions are made to GenBank using BankIt, which is a Web- d.ncbi.nlm.nih.g
based form, or the stand-alone submission program, Sequin. Upon
ov/21071399)
receipt of a sequence submission, the GenBank staff examines the
originality of the data and assigns an accession number to the Release date 1982
sequence and performs quality assurance checks. The submissions Access
are then released to the public database, where the entries are
Data format XML
retrievable by Entrez or downloadable by FTP. Bulk submissions
of Expressed Sequence Tag (EST), Sequence-tagged site (STS), ASN.1
Genome Survey Sequence (GSS), and High-Throughput Genome Genbank format
Sequence (HTGS) data are most often submitted by large-scale
sequencing centers. The GenBank direct submissions group also Website NCBI (https://w
processes complete microbial genome sequences.[6][7] ww.ncbi.nlm.nih.
gov/)

History Download URL ncbi ftp (http://ft

p.ncbi.nih.gov/)
Walter Goad of the Theoretical Biology and Biophysics Group at Web service URL eutils (http://euti
Los Alamos National Laboratory (LANL) and others established ls.ncbi.nlm.nih.g
the Los Alamos Sequence Database in 1979, which culminated in ov/)
1982 with the creation of the public GenBank.[8] Funding was
soap (http://eutil
provided by the National Institutes of Health, the National Science
s.ncbi.nlm.nih.g
Foundation, the Department of Energy, and the Department of ov/soap/v2.0/eu
Defense. LANL collaborated on GenBank with the firm Bolt, tils.wsdl)
Beranek, and Newman, and by the end of 1983 more than 2,000
Tools
sequences were stored in it.
Web BLAST
In the mid 1980s, the Intelligenetics bioinformatics company at Standalone
BLAST
Stanford University managed the GenBank project in
collaboration with LANL.[9] As one of the earliest bioinformatics Miscellaneous
community projects on the Internet, the GenBank project started License Unclear[1]
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]

Growth
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.

Genbank and EMBL: NucleotideSequences

1986/1987 Volumes I to VII.

CD-ROM of Genbank v100

 Top 20 organisms in GenBank (Release 250)[5]
Organism base pairs

Triticum aestivum 2.15443744183 × 1011

SARS-CoV-2 1.65771825746 × 1011

Hordeum vulgare subsp. vulgare 1.01344340096 × 1011

Mus musculus 3.0614386913 × 1010

Homo sapiens 2.7834633853 × 1010

Growth in GenBank base pairs, 1982
Avena sativa 2.1127939362 × 1010 to 2018, on a semi-log scale
Escherichia coli 1.5517830491 × 1010

Klebsiella pneumoniae 1.1144687122 × 1010

Danio rerio 1.0890148966 × 1010

Bos taurus 1.0650671156 × 1010

Triticum turgidum subsp. durum 9.981529154 × 109

Zea mays 7.412263902 × 109

Avena insularis 6.924307246 × 109

Secale cereale 6.749247504 × 109

Rattus norvegicus 6.548854408 × 109

Aegilops longissima 5.920483689 × 109

Canis lupus familiaris 5.776499164 × 109

Aegilops sharonensis 5.272476906 × 109

Sus scrofa 5.179074907 × 109

Rhinatrema bivittatum 5.178626132 × 109

Incomplete identifications
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]

See also
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

References
1. The download page (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/) 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."
2. Eric W Sayers; Mark Cavanaugh; Karen Clark; Kim D Pruitt; Conrad L Schoch; Stephen T
Sherry; Ilene Karsch-Mizrachi (7 January 2022). "GenBank" (https://doi.org/10.1093%2Fna
r%2Fgkab1135). Nucleic Acids Archive. 50 (D1): D161–D164. doi:10.1093/nar/gkab1135 (ht
tps://doi.org/10.1093%2Fnar%2Fgkab1135).
3. Benson D; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L.; et al. (2008).
"GenBank" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238942). Nucleic Acids
Research. 36 (Database): D25–D30. doi:10.1093/nar/gkm929 (https://doi.org/10.1093%2Fn
ar%2Fgkm929). PMC 2238942 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238942).
PMID 18073190 (https://pubmed.ncbi.nlm.nih.gov/18073190).
4. Benson D; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W.; et al. (2009).
"GenBank" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686462). Nucleic Acids
Research. 37 (Database): D26–D31. doi:10.1093/nar/gkn723 (https://doi.org/10.1093%2Fna
r%2Fgkn723). PMC 2686462 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686462).
PMID 18940867 (https://pubmed.ncbi.nlm.nih.gov/18940867).
5. "GenBank release notes (Release 250)" (http://ftp.ncbi.nih.gov/genbank/gbrel.txt). NCBI. 15
June 2022. Retrieved 20 July 2022.
6. "How to submit data to GenBank" (https://www.ncbi.nlm.nih.gov/genbank/submit/). NCBI.
Retrieved 20 July 2022.
 7. "GenBank Submission Types" (https://www.ncbi.nlm.nih.gov/genbank/submit_types/). NCBI.
Retrieved 20 July 2022.
8. Hanson, Todd (2000-11-21). "Walter Goad, GenBank founder, dies" (http://www.lanl.gov/org
s/pa/News/112100.html). Newsbulletin: obituary. Los Alamos National Laboratory.
9. LANL GenBank History (http://www.bio.net/bionet/mm/bionews/1994-January/000877.html)
10. Benton D (1990). "Recent changes in the GenBank On-line Service" (https://www.ncbi.nlm.n
ih.gov/pmc/articles/PMC330520). Nucleic Acids Research. 18 (6): 1517–1520.
doi:10.1093/nar/18.6.1517 (https://doi.org/10.1093%2Fnar%2F18.6.1517). PMC 330520 (htt
ps://www.ncbi.nlm.nih.gov/pmc/articles/PMC330520). PMID 2326192 (https://pubmed.ncbi.nl
m.nih.gov/2326192).
11. Benson, D. A.; Cavanaugh, M.; Clark, K.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.;
Sayers, E. W. (2012). "GenBank" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531190).
Nucleic Acids Research. 41 (Database issue): D36–D42. doi:10.1093/nar/gks1195 (https://d
oi.org/10.1093%2Fnar%2Fgks1195). PMC 3531190 (https://www.ncbi.nlm.nih.gov/pmc/articl
es/PMC3531190). PMID 23193287 (https://pubmed.ncbi.nlm.nih.gov/23193287).
12. Kyung Sun Park; Chang-Seok Ki; Cheol-In Kang; Yae-Jean Kim; Doo Ryeon Chung; Kyong
Ran Peck; Jae-Hoon Song; Nam Yong Lee (May 2012). "Evaluation of the GenBank,
EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates
That Were Unidentifiable or Misidentified by Conventional Methods" (https://www.ncbi.nlm.ni
h.gov/pmc/articles/PMC3347139). J. Clin. Microbiol. 50 (5): 1792–1795.
doi:10.1128/JCM.00081-12 (https://doi.org/10.1128%2FJCM.00081-12). PMC 3347139 (http
s://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347139). PMID 22403421 (https://pubmed.ncbi.
nlm.nih.gov/22403421).
13. EzTaxon-e Database (https://web.archive.org/web/20130928154318/http://eztaxon-e.ezbiocl
oud.net/) eztaxon-e.ezbiocloud.net (archive accessed 25 March 2021)
14. leBIBI V5 (https://web.archive.org/web/20151001000357/http://pbil.univ-lyon1.fr/bibi/)
pbil.univ-lyon1.fr (archive accessed 25 March 2021)
15. Ogwang, Joel; Bariche, Michel; Bos, Arthur R. (2021). "Genetic diversity and phylogenetic
relationships of threadfin breams (Nemipterus spp.) from the Red Sea and eastern
Mediterranean Sea" (https://cdnsciencepub.com/doi/full/10.1139/gen-2019-0163). Genome.
64 (3): 207–216. doi:10.1139/gen-2019-0163 (https://doi.org/10.1139%2Fgen-2019-0163).
16. van den Burg, Matthijs P.; Herrando-Pérez, Salvador; Vieites, David R. (13 August 2020).
"ACDC, a global database of amphibian cytochrome-b sequences using reproducible
curation for GenBank records" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426930).
Scientific Data. 7 (1). doi:10.1038/s41597-020-00598-9 (https://doi.org/10.1038%2Fs41597-
020-00598-9). eISSN 2052-4463 (https://www.worldcat.org/issn/2052-4463). PMC 7426930
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7426930). PMID 32792559 (https://pubmed.
ncbi.nlm.nih.gov/32792559).
17. Li, Xiaobing; Shen, Xuejuan; Chen, Xiao; Xiang, Dan; Murphy, Robert W.; Shen, Yongyi (6
February 2018). "Detection of Potential Problematic Cytb Gene Sequences of Fishes in
GenBank" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5808227). Frontiers in Genetics.
9. doi:10.3389/fgene.2018.00030 (https://doi.org/10.3389%2Ffgene.2018.00030).
eISSN 1664-8021 (https://www.worldcat.org/issn/1664-8021). PMC 5808227 (https://www.nc
bi.nlm.nih.gov/pmc/articles/PMC5808227). PMID 29467794 (https://pubmed.ncbi.nlm.nih.go
v/29467794).
18. Heller, Philip; Casaletto, James; Ruiz, Gregory; Geller, Jonathan (7 August 2018). "A
database of metazoan cytochrome c oxidase subunit I gene sequences derived from
GenBank with CO-ARBitrator" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6080493).
Scientific Data. 5 (1). doi:10.1038/sdata.2018.156 (https://doi.org/10.1038%2Fsdata.2018.15
6). eISSN 2052-4463 (https://www.worldcat.org/issn/2052-4463). PMC 6080493 (https://ww
w.ncbi.nlm.nih.gov/pmc/articles/PMC6080493). PMID 30084847 (https://pubmed.ncbi.nlm.ni
h.gov/30084847).
19. Van Den Burg, Matthijs P.; Vieites, David R. (22 September 2022). "Bird genetic databases
need improved curation and error reporting to <scp>NCBI</scp>" (https://doi.org/10.1111%2
Fibi.13143). Ibis. doi:10.1111/ibi.13143 (https://doi.org/10.1111%2Fibi.13143). eISSN 1474-
919X (https://www.worldcat.org/issn/1474-919X). ISSN 0019-1019 (https://www.worldcat.or
g/issn/0019-1019).

 This article incorporates public domain material from NCBI Handbook (https://www.ncbi.nl
m.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=handbook.TOC&depth=2). National
Center for Biotechnology Information.

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

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