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. 2017 Jan 4;45(D1):D37-D42.
doi: 10.1093/nar/gkw1070. Epub 2016 Nov 28.

GenBank

Dennis A Benson  1 , Mark Cavanaugh  1 , Karen Clark  1 , Ilene Karsch-Mizrachi  1 , David J Lipman  1 , James Ostell  1 , Eric W Sayers  2
Affiliations

GenBank

Dennis A Benson et al. Nucleic Acids Res. .

Abstract

GenBank® (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for 370 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or the NCBI Submission Portal. GenBank staff assign accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Nucleotide database, which links to related information such as taxonomy, genomes, protein sequences and structures, and biomedical journal literature in PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP. Recent updates include changes to policies regarding sequence identifiers, an improved 16S submission wizard, targeted loci studies, the ability to submit methylation and BioNano mapping files, and a database of anti-microbial resistance genes.

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References

    1. Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2016;44:D67–D72. - PMC - PubMed
    1. Gibson R., Alako B., Amid C., Cerdeno-Tarraga A., Cleland I., Goodgame N., Ten Hoopen P., Jayathilaka S., Kay S., Leinonen R., et al. Biocuration of functional annotation at the European nucleotide archive. Nucleic Acids Res. 2016;44:D58–D66. - PMC - PubMed
    1. Mashima J., Kodama Y., Kosuge T., Fujisawa T., Katayama T., Nagasaki H., Okuda Y., Kaminuma E., Ogasawara O., Okubo K., et al. DNA data bank of Japan (DDBJ) progress report. Nucleic Acids Res. 2016;44:D51–D57. - PMC - PubMed
    1. Cochrane G., Karsch-Mizrachi I., Takagi T., International Nucleotide Sequence Database, C. The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2016;44:D48–D50. - PMC - PubMed
    1. NCBI Resource Coordinators. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2016;44:D7–D19. - PMC - PubMed

Publication types