GenBank

Last updated
GenBank
Content
DescriptionNucleotide sequences for more than 300,000 organisms with supporting bibliographic and biological annotation.
Data types
captured
  • Nucleotide sequence
  • Protein sequence
Organisms All
Contact
Research center NCBI
Primary citation PMID   21071399
Release date1982;41 years ago (1982)
Access
Data format
Website NCBI
Download URL ncbi ftp
Web service URL
Tools
Web BLAST
Standalone BLAST
Miscellaneous
License Unclear [1]

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).

Contents

GenBank and its collaborators will receive sequences produced in laboratories throughout the world from more than 500,000 formally described species. [2] 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. [3] [4]

Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. [5] 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 (HTGS) data are most often submitted by large-scale sequencing centers. The GenBank direct submissions group also processes complete microbial genome sequences. [6] [7]

History

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. [8] 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. [9] 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). [10]

Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII. NucleotideSequences 86 87.jpeg
Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.
CD-ROM of Genbank v100 Genbank100CD.jpg
CD-ROM of Genbank v100

Growth

Growth in GenBank base pairs, 1982 to 2018, on a semi-log scale Growth of Genbank.svg
Growth in GenBank base pairs, 1982 to 2018, on a 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". [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.

Top 20 organisms in GenBank (Release 250) [5]
Organism base pairs
Triticum aestivum 2.15443744183×10^11
SARS-CoV-2 1.65771825746×10^11
Hordeum vulgare subsp. vulgare1.01344340096×10^11
Mus musculus 3.0614386913×10^10
Homo sapiens 2.7834633853×10^10
Avena sativa 2.1127939362×10^10
Escherichia coli 1.5517830491×10^10
Klebsiella pneumoniae 1.1144687122×10^10
Danio rerio 1.0890148966×10^10
Bos taurus 1.0650671156×10^10
Triticum turgidum subsp. durum9.981529154×10^9
Zea mays 7.412263902×10^9
Avena insularis 6.924307246×10^9
Secale cereale 6.749247504×10^9
Rattus norvegicus 6.548854408×10^9
Aegilops longissima 5.920483689×10^9
Canis lupus familiaris 5.776499164×10^9
Aegilops sharonensis 5.272476906×10^9
Sus scrofa 5.179074907×10^9
Rhinatrema bivittatum 5.178626132×10^9

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

Related Research Articles

<span class="mw-page-title-main">National Center for Biotechnology Information</span> Database branch of the US National Library of Medicine

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. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.

In the field of bioinformatics, a sequence database is a type of biological database that is composed of a large collection of computerized ("digital") nucleic acid sequences, protein sequences, or other polymer sequences stored on a computer. The UniProt database is an example of a protein sequence database. As of 2013 it contained over 40 million sequences and is growing at an exponential rate. Historically, sequences were published in paper form, but as the number of sequences grew, this storage method became unsustainable.

In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes.

In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination. The identification of ESTs has proceeded rapidly, with approximately 74.2 million ESTs now available in public databases. EST approaches have largely been superseded by whole genome and transcriptome sequencing and metagenome sequencing.

<span class="mw-page-title-main">Entrez</span> Cross-database search engine for health sciences

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. The NCBI is a part of the National Library of Medicine (NLM), which is itself a department of the National Institutes of Health (NIH), which in turn is a part of the United States Department of Health and Human Services. The name "Entrez" was chosen to reflect the spirit of welcoming the public to search the content available from the NLM.

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: NIG's DNA Data Bank of Japan (Japan), NCBI's GenBank (USA) and the EMBL-EBI's European Nucleotide Archive (UK). New and updated data on nucleotide sequences contributed by research teams to each of the three databases are synchronized on a daily basis through continuous interaction between the staff at each the collaborating organizations.

The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.

<span class="mw-page-title-main">David J. Lipman</span> American biologist

David J. Lipman is an American biologist who from 1989 to 2017 was the director of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. NCBI is the home of GenBank, the U.S. node of the International Sequence Database Consortium, and PubMed, one of the most heavily used sites in the world for the search and retrieval of biomedical information. Lipman is one of the original authors of the BLAST sequence alignment program, and a respected figure in bioinformatics. In 2017, he left NCBI and became Chief Science Officer at Impossible Foods.

The DNA Data Bank of Japan (DDBJ) is a biological database that collects DNA sequences. It is located at the National Institute of Genetics (NIG) in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC. It exchanges its data with European Molecular Biology Laboratory at the European Bioinformatics Institute and with GenBank at the National Center for Biotechnology Information on a daily basis. Thus these three databanks contain the same data at any given time.

<span class="mw-page-title-main">MicrobesOnline</span>

MicrobesOnline is a publicly and freely accessible website that hosts multiple comparative genomic tools for comparing microbial species at the genomic, transcriptomic and functional levels. MicrobesOnline was developed by the Virtual Institute for Microbial Stress and Survival, which is based at the Lawrence Berkeley National Laboratory in Berkeley, California. The site was launched in 2005, with regular updates until 2011.

The Reference Sequence (RefSeq) database is an open access, annotated and curated collection of publicly available nucleotide sequences and their protein products. RefSeq was introduced in 2000. This database is built by National Center for Biotechnology Information (NCBI), and, unlike GenBank, provides only a single record for each natural biological molecule for major organisms ranging from viruses to bacteria to eukaryotes.

dbSNP Genetics database

The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Although the name of the database implies a collection of one class of polymorphisms only, it in fact contains a range of molecular variation: (1) SNPs, (2) short deletion and insertion polymorphisms (indels/DIPs), (3) microsatellite markers or short tandem repeats (STRs), (4) multinucleotide polymorphisms (MNPs), (5) heterozygous sequences, and (6) named variants. The dbSNP accepts apparently neutral polymorphisms, polymorphisms corresponding to known phenotypes, and regions of no variation. It was created in September 1998 to supplement GenBank, NCBI’s collection of publicly available nucleic acid and protein sequences.

<span class="mw-page-title-main">Sequence Read Archive</span>

The Sequence Read Archive is a bioinformatics database that provides a public repository for DNA sequencing data, especially the "short reads" generated by high-throughput sequencing, which are typically less than 1,000 base pairs in length. The archive is part of the International Nucleotide Sequence Database Collaboration (INSDC), and run as a collaboration between the NCBI, the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ).

<span class="mw-page-title-main">European Nucleotide Archive</span> Online database from the EBI on Nucleotides

The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.

The ascidian mitochondrial code is a genetic code found in the mitochondria of Ascidia.

Donna R. Maglott is a staff scientist at the National Center for Biotechnology Information known for her research on large-scale genomics projects, including the mouse genome and development of databases required for genomics research.

In molecular phylogenetics, relationships among individuals are determined using character traits, such as DNA, RNA or protein, which may be obtained using a variety of sequencing technologies. High-throughput next-generation sequencing has become a popular technique in transcriptomics, which represent a snapshot of gene expression. In eukaryotes, making phylogenetic inferences using RNA is complicated by alternative splicing, which produces multiple transcripts from a single gene. As such, a variety of approaches may be used to improve phylogenetic inference using transcriptomic data obtained from RNA-Seq and processed using computational phylogenetics.

VFDB also known as Virulence Factor Database is a database that provides scientist quick access to virulence factors in bacterial pathogens. It can be navigated and browsed using genus or words. A BLAST tool is provided for search against known virulence factors. VFDB contains a collection of 16 important bacterial pathogens. Perl scripts were used to extract positions and sequences of VF from GenBank. Clusters of Orthologous Groups (COG) was used to update incomplete annotations. More information was obtained by NCBI. VFDB was built on Linux operation systems on DELL PowerEdge 1600SC servers.

<span class="mw-page-title-main">Genome mining</span>

Genome mining describes the exploitation of genomic information for the discovery of biosynthetic pathways of natural products and their possible interactions. It depends on computational technology and bioinformatics tools. The mining process relies on a huge amount of data accessible in genomic databases. By applying data mining algorithms, the data can be used to generate new knowledge in several areas of medicinal chemistry, such as discovering novel natural products.

References

  1. ↑ The download page 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". Nucleic Acids Archive. 50 (D1): D161–D164. doi: 10.1093/nar/gkab1135 .
  3. ↑ Benson D; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Wheeler, D. L.; et al. (2008). "GenBank". Nucleic Acids Research. 36 (Database): D25–D30. doi:10.1093/nar/gkm929. PMC   2238942 . PMID   18073190.
  4. ↑ Benson D; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W.; et al. (2009). "GenBank". Nucleic Acids Research. 37 (Database): D26–D31. doi:10.1093/nar/gkn723. PMC   2686462 . PMID   18940867.
  5. 1 2 3 4 "GenBank release notes (Release 250)". NCBI. 15 June 2022. Retrieved 20 July 2022.
  6. ↑ "How to submit data to GenBank". NCBI. Retrieved 20 July 2022.
  7. ↑ "GenBank Submission Types". NCBI. Retrieved 20 July 2022.
  8. ↑ Hanson, Todd (2000-11-21). "Walter Goad, GenBank founder, dies". Newsbulletin: obituary. Los Alamos National Laboratory.
  9. ↑ LANL GenBank History
  10. ↑ Benton D (1990). "Recent changes in the GenBank On-line Service". Nucleic Acids Research. 18 (6): 1517–1520. doi:10.1093/nar/18.6.1517. PMC   330520 . PMID   2326192.
  11. ↑ Benson, D. A.; Cavanaugh, M.; Clark, K.; Karsch-Mizrachi, I.; Lipman, D. J.; Ostell, J.; Sayers, E. W. (2012). "GenBank". Nucleic Acids Research. 41 (Database issue): D36–D42. doi:10.1093/nar/gks1195. PMC   3531190 . PMID   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". J. Clin. Microbiol. 50 (5): 1792–1795. doi:10.1128/JCM.00081-12. PMC   3347139 . PMID   22403421.
  13. ↑ EzTaxon-e Database eztaxon-e.ezbiocloud.net (archive accessed 25 March 2021)
  14. ↑ leBIBI V5 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". Genome. 64 (3): 207–216. doi:10.1139/gen-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". Scientific Data. 7 (1): 268. doi:10.1038/s41597-020-00598-9. eISSN   2052-4463. PMC   7426930 . PMID   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". Frontiers in Genetics. 9: 30. doi: 10.3389/fgene.2018.00030 . eISSN   1664-8021. PMC   5808227 . PMID   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". Scientific Data. 5 (1). doi:10.1038/sdata.2018.156. eISSN   2052-4463. PMC   6080493 . PMID   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>". Ibis. doi: 10.1111/ibi.13143 . eISSN   1474-919X. ISSN   0019-1019.
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