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. 2016 Jan 4;44(D1):D67-72.
doi: 10.1093/nar/gkv1276. Epub 2015 Nov 20.

GenBank

Karen Clark  1 , Ilene Karsch-Mizrachi  1 , David J Lipman  1 , James Ostell  1 , Eric W Sayers  2
Affiliations

GenBank

Karen Clark et al. Nucleic Acids Res. .

Abstract

GenBank(®) (www.ncbi.nlm.nih.gov/genbank/) is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species. Recent developments include a new starting page for submitters, a shift toward using accession.version identifiers rather than GI numbers, a wizard for submitting 16S rRNA sequences, and an Identical Protein Report to address growing issues of data redundancy. GenBank organizes the sequence data received from individual laboratories and large-scale sequencing projects into 18 divisions, and GenBank staff assign unique accession.version identifiers upon data receipt. Most submitters use the web-based BankIt or standalone Sequin programs. 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 nuccore, nucest, and nucgss databases of the Entrez retrieval system, which integrates these records with a variety of other data including taxonomy nodes, genomes, protein 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.

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References

    1. Benson D.A., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2015;43:D30–D35. - PMC - PubMed
    1. Silvester N., Alako B., Amid C., Cerdeno-Tarraga A., Cleland I., Gibson R., Goodgame N., Ten Hoopen P., Kay S., Leinonen R., et al. Content discovery and retrieval services at the European Nucleotide Archive. Nucleic Acids Res. 2015;43:D23–D29. - PMC - PubMed
    1. Kosuge T., Mashima J., Kodama Y., Fujisawa T., Kaminuma E., Ogasawara O., Okubo K., Takagi T., Nakamura Y. DDBJ progress report: a new submission system for leading to a correct annotation. Nucleic Acids Res. 2014;42:D44–D49. - PMC - PubMed
    1. Nakamura Y., Cochrane G., Karsch-Mizrachi I., International Nucleotide Sequence Database, C. The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2013;41:D21–D24. - PMC - PubMed
    1. NCBI Resource Coordinators. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2016 doi:10.1093/nar/gkv1290. - PMC - PubMed

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