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The GenBank sequence database is an
open access Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre o ...
, annotated collection of all publicly available
nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecul ...
sequences and their
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
translations. It is produced and maintained by the
National Center for Biotechnology Information The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. T ...
(NCBI; a part of the
National Institutes of Health The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government The federal government of the United States (U.S. federal government or U ...
in the
United States The United States of America (U.S.A. or USA), commonly known as the United States (U.S. or US) or America, is a country primarily located in North America. It consists of 50 U.S. state, states, a Washington, D.C., federal district, five ma ...
) as part of the
International Nucleotide Sequence Database Collaboration The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It involves the following computerized databases: DNA Data Bank of Japan (Japan) ...
(INSDC). GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 500,000 formally described
species In biology, a species is the basic unit of Taxonomy (biology), classification and a taxonomic rank of an organism, as well as a unit of biodiversity. A species is often defined as the largest group of organisms in which any two individuals of ...
. The database started in 1982 by
Walter Goad Walter Goad (1925–2000) was a nuclear physicist at the Los Alamos National Laboratory. During the 1960s, Goad turned his attention from physics to biology and he is best known for his contributions to the founding of GenBank, the most widely us ...
and
Los Alamos National Laboratory Los Alamos National Laboratory (often shortened as Los Alamos and LANL) is one of the sixteen research and development laboratories of the United States Department of Energy (DOE), located a short distance northwest of Santa Fe, New Mexico, i ...
. 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. Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. 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 This is a list of academic journals published by MDPI. As of September 2022, MDPI publishes 399 peer-reviewed academic journals and nine conference journals. {, class="wikitable sortable" , +List of MDPI journals !Journal name !Subject ...
(HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences.


History

Walter Goad Walter Goad (1925–2000) was a nuclear physicist at the Los Alamos National Laboratory. During the 1960s, Goad turned his attention from physics to biology and he is best known for his contributions to the founding of GenBank, the most widely us ...
of the Theoretical Biology and Biophysics Group at
Los Alamos National Laboratory Los Alamos National Laboratory (often shortened as Los Alamos and LANL) is one of the sixteen research and development laboratories of the United States Department of Energy (DOE), located a short distance northwest of Santa Fe, New Mexico, i ...
(LANL) and others established the Los Alamos Sequence Database in 1979, which culminated in 1982 with the creation of the public GenBank. Funding was provided by the
National Institutes of Health The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government The federal government of the United States (U.S. federal government or U ...
, the National Science Foundation, the Department of Energy, and the Department of Defense. LANL collaborated on GenBank with the firm
Bolt, Beranek, and Newman Raytheon BBN (originally Bolt Beranek and Newman Inc.) is an American research and development company, based next to Fresh Pond in Cambridge, Massachusetts, United States. In 1966, the Franklin Institute awarded the firm the Frank P. Brown ...
, 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.LANL GenBank History
/ref> As one of the earliest
bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combin ...
community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting
open access Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre o ...
communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information (NCBI).


Growth

The GenBank
release notes Release notes are documents that are distributed with software products or hardware products, sometimes when the product is still in the development or test state (e.g., a beta release). For products that have already been in use by clients, the r ...
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". As of 15 June 2022, GenBank release 250.0 has over 239 million
loci Locus (plural loci) is Latin for "place". It may refer to: Entertainment * Locus (comics), a Marvel Comics mutant villainess, a member of the Mutant Liberation Front * ''Locus'' (magazine), science fiction and fantasy magazine ** '' Locus Award ...
, 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.


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'' 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 and the BIBI 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. 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. 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 Birds are a group of warm-blooded vertebrates constituting the class Aves (), characterised by feathers, toothless beaked jaws, the laying of hard-shelled eggs, a high metabolic rate, a four-chambered heart, and a strong yet lightweig ...
further showed that 45% of the identified erroneous records lack a voucher specimen that prevents a reassessment of the species identification.


See also

*
Ensembl Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other ...
* Human Protein Reference Database (HPRD) * Sequence analysis *
UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived fro ...
* 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

*


External links


GenBankExample sequence record, for hemoglobin betaBankIt
— 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?
{{Authority control National Institutes of Health Genetics databases Genome databases Bioinformatics Biological databases