GenBank

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.{{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}}{{Cite web |title=GenBank Submission Types |url=https://www.ncbi.nlm.nih.gov/genbank/submit_types/ |access-date=20 July 2022 |website=NCBI}}

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.{{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}} 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.[http://www.bio.net/bionet/mm/bionews/1994-January/000877.html LANL GenBank History] 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).{{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}}

File:NucleotideSequences 86 87.jpeg

File:Genbank100CD.jpg

Image:Growth of Genbank.svg]]

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".{{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}}{{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

}} As of 15 June 2022, GenBank release 250.0 has over 239 million loci, 1,39 trillion nucleotide bases, from 239 million reported sequences.

The GenBank database includes additional data sets that are constructed mechanically from the main sequence data collection, and therefore are excluded from this count.

An analysis of Genbank and other services for the molecular identification of clinical blood culture isolates using 16S rRNA sequences{{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}} showed that such analyses were more discriminative when GenBank was combined with other services such as EzTaxon-e[https://web.archive.org/web/20130928154318/http://eztaxon-e.ezbiocloud.net/ EzTaxon-e Database] eztaxon-e.ezbiocloud.net (archive accessed 25 March 2021) and the BIBI[https://web.archive.org/web/20151001000357/http://pbil.univ-lyon1.fr/bibi/ leBIBI V5] pbil.univ-lyon1.fr (archive accessed 25 March 2021) 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.{{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}} 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.{{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 = }}{{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 }}{{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 = }} 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.{{cite journal | last1 = Van Den Burg | first1 = Matthijs P. | last2 = Vieites | first2 = David R. | title = Bird genetic databases need improved curation and error reporting to NCBI | 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 }}

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.{{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}}

• 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

{{reflist|30em}}

• {{NCBI-handbook}}

• [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] — a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.
• [http://emboss.sourceforge.net EMBOSS] — 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