Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
National Library of Medicine / National Institutes of Health. Offers many important databases (PubMed, GenBank, OMIM) and some tools.
GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations.
GenBank (R) is a comprehensive database that contains publicly available nucleotide sequences for more than 240 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing 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 EMBL Data Library in Europe and the DNA Data Bank of Japan ensures worldwide coverage. GenBank is accessible through NCBI’s retrieval system, Entrez, 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 access GenBank and its related retrieval and analysis services, begin at the NCBI.
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), and other high-throughput data from sequencing centers.
The US Office of Patents and Trademarks also contributes sequences from issued patents. GenBank, the EMBL Data Library (2) in Europe, and the DNA Databank of Japan (DDBJ) (3) comprise the International Nucleotide Sequence Databases, and are members of a long-standing collaboration in which information is exchanged daily to ensure a uniform and comprehensive collection of sequence information. NCBI makes the GenBank data available at no cost over the Internet, via FTP and via a wide range of web-based retrieval and analysis services which operate on the GenBank data.
he GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, 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.
About one-third of author submissions are received through NCBI’s web-based data submission tool, BankIt (www.ncbi.nlm.nih.gov/BankIt). Using BankIt, authors enter sequence information directly into a form, and add biological annotations such as coding regions, or mRNA features. Free-form text boxes, list boxes, and pull-down menus allow the submitter to further describe the sequence without having to learn formatting rules or restricted vocabularies. BankIt validates submissions, flagging many common errors, and checks for vector contamination using a variant of BLAST called Vecscreen, before creating a draft record in GenBank flat file format for the submitter to review. BankIt is the tool of choice for simple submissions, especially when only one or a small number of records is to be submitted (7). BankIt can also be used by submitters to update their existing GenBank records.