GenBank Database

The GenBank Database is an Entity Database of Genetic Sequences.

• Context:
  • It is accessible through NCBI's retrieval system, Entrez.
  • A set of GI numbers (with redundancies) used in recent literature can be found in ftp://ftp.ncbi.nih.gov/genbank/
  • It contains redundant entries and unconfirmed sequences.
  • Are used more often than TREMBL IDs.
  • The .faa files would contain the IDs and protein names/descriptions, and protein sequences.
• Example(s):
  • http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
• See: FASTA File Format, SIMAP Database, UniProt Database, NIH, Protein Sequence.

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References

2009

• (Wikipedia, 2009) ⇒ http://en.wikipedia.org/wiki/GenBank
  • The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced at National Center for Biotechnology Information (NCBI) as part of the International Nucleotide Sequence Database Collaboration, or INSDC. GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. GenBank continues to grow at an exponential rate, doubling every 18 months. Release 155, produced in August 2006, contained over 65 billion nucleotide bases in more than 61 million sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers.

2005

• D. Maglott et. al. Entrez Gene. (2005). “Gene-centered information at NCBI. Nucleic Acids Res. January 1; 2005.
• http://www.ncbi.nlm.nih.gov/Genbank/
  • GenBank® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2008 Jan;36(Database issue):D25-30).
  • There are approximately 85,759,586,764 bases in 82,853,685 sequence records in the traditional GenBank divisions and 108,635,736,141 bases in 27,439,206 sequence records in the WGS division as of February 2008.
  • The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months.
  • GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI.
  • An example of a GenBank record may be viewed for a Saccharomyces cerevisiae gene. http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html
  • Each GenBank entry includes a concise description of the sequence, the scientific name and taxonomy of the source organism, and a table of features that identifies coding regions and other sites of biological significance, such as transcription units, sites of mutations or modifications, and repeats. Protein translations for coding regions are included in the feature table. Bibliographic references are included along with a link to the Medline unique identifier for all published sequences.

• http://www.psc.edu/general/software/packages/genbank/genbank.html

2004

• Dennis A. Benson, Ilene Karsch-Mizrachi, David J. Lipman, James Ostell, and David L. Wheeler. (2004). “GenBank: update." Nucleic Acids Res. 2004 January 1; 32(Database issue): D23–D26. doi:10.1093/nar/gkh045.
  • GenBank (R) is a comprehensive database that contains publicly available DNA sequences for more than 140 000 named organisms, obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects. Most submissions are made using the BankIt (web) or Sequin program and accession numbers are assigned by GenBank staff upon receipt. Daily data exchange with the EMBL Data Library in the UK and the DNA Data Bank of Japan helps ensure 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, go to the NCBI home page at: http://www.ncbi.nlm.nih.gov.

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