Biotecnologia

D48–D53 Nucleic Acids Research, 2012, Vol. 40, Database issue doi:10.1093/nar/gkr1202

Published online 5 December 2011

GenBank
Dennis A. Benson, Ilene Karsch-Mizrachi, Karen Clark, David J. Lipman, James Ostell and Eric W. Sayers*
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD20894, USA
Received September 30, 2011; Revised November 14, 2011; Accepted November 17, 2011

ABSTRACT GenBankÕ is a comprehensive database that contains publicly available nucleotide sequences for more than 250 000 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 standalone Sequin programs, and accession numbers are assigned by GenBank staff upon 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 Entrez retrievalsystem, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via 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. To accessGenBank and its related retrieval and analysis services, begin at the NCBI home page: www.ncbi.nlm.nih.gov. INTRODUCTION GenBank (1) is a comprehensive public database of nucleotide sequences and supporting bibliographic and biological annotation. GenBank is built and distributed by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine (NLM),located on the campus of the US National Institutes of Health (NIH) in Bethesda, MD, USA. NCBI builds GenBank primarily from the submission of sequence data from authors and from the bulk submission of expressed sequence tag (EST), genome survey

sequence (GSS), whole-genome shotgun (WGS) and other high-throughput data from sequencing centers. The US Office of Patents and Trademarks also contributessequences from issued patents. GenBank participates with the EMBL Nucleotide Sequence Database (EMBL-Bank), part of the European Nucleotide Archive (ENA) (2), and the DNA Data Bank of Japan (DDBJ) (3) as a partner in the International Nucleotide Sequence Database Collaboration (INSDC). The INSDC partners exchange data daily to ensure that a uniform and comprehensive collection of sequenceinformation is available worldwide. NCBI makes the GenBank data available at no cost over the Internet, through FTP and a wide range of web-based retrieval and analysis services (4). RECENT DEVELOPMENTS PopSet redesign In the past year, NCBI redesigned the web interface for the PopSet database (www.ncbi.nlm.nih.gov/popset) of related sequences and alignments derived from phylogenetic, population, mutationand ecosystem studies that have been submitted to GenBank. The new PopSet record views contain three sections: an introduction showing the title and citation for the citation reporting the data set; a list of sequences contained in the data set; and, when available, an alignment of the sequences shown in the same Graphical Sequence Viewer that is a display option on nucleotide and protein records.In addition, PopSet record pages now display links to other PopSet records reported in the same published study, making it much easier to locate these related records. For PopSet records with fewer than 100 sequences, links are provided to generate a BLAST alignment of the sequences or, if an alignment was submitted as part of the record, a distance tree view of the alignment. New tools for...