GenBank

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.1

Description

GenBank depends on its contributors to help keep the database as comprehensive, current, and accurate as possible. NCBI (National Center for Biotechnology Information) provides timely and accurate processing and biological review of new entries and updates to existing entries, and is ready to assist authors who have new data to submit.2

        1 atgaggctcg cttaccttct cctactgctt gtggccgtgt tgttccaagc tgggggcgga
       61 tcagccaaac ccataatgtt cttcgaaatg caagcctgct ggtcccacag cggcgtctgc
      121 agagacaaga gtgaaaggaa ttgcaagccg atggcgtgga cctactgtga aaaccggaac
      181 cagaaatgct gcgactccgg ccacagctgt cgtgtcatcg tcatgaggct cacttacctt
      241 ctcctactgc ttgtggccgt gttgttccag gctgggagtg gatcagccga acccatattc
      301 ttctatggac gccaaccctg ctcgtactac gacggggtct gccgagacaa aagcgatgtg
      361 aattgcaaat atatcgcgtt cacctactgt gaaaacccga accagagatg ctgctactac
      421 tag

          mRNA gene sequence of a peptide from platypus venom Ornithorhynchus anatinus.3

Many journals require submission of sequence information to a database prior to publication so that an accession number may appear in the paper. Software is provided. There are specialized, streamlined procedures for batch submissions of sequences, such as EST, STS, and GSS sequences. Revisions or updates to GenBank entries can be made at any time. 4

GenBank is available for searching at NCBI via several methods.

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. These three organizations exchange data on a daily basis.5

Function

• Taxonomy
  • Identification tools
• User interface
  • Personal and institutional
  • Raw data

Why use this tool?

• GenBank should be used to store gene sequence data prior to publication.
• Data in GenBank can be used for taxonomy

Who will use this tool?

• Data creation
  • Experts - taxonomy
• Data users
  • Expert

How will the tool be used?

Tools are available for submission:6

• Sequin Stand-alone sequence submission tool
• BankIt  A web submission tool for quick and simple submissions
• tbl2asn Command-line sequence submission tool

 Batch submission is available

GenBank divisions

• dbEST accepts Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA).7
• dbGSS is similar in nature to the EST division, except that its sequences are genomic in origin, rather than cDNA (mRNA).8
• dbSTS accepts short (about 200-500 bp) sequences that are operationally unique in a genome (i.e., can be specifically detected by PCR in the presence of all other genomic sequences), and that define a specific position on the physical map.

Searching

• Entrez Browser GenBank (nucleotides and proteins), PubMed (MEDLINE), 3D structures, genomes, and PopSet databases
• BLAST Sequence Similarity Searching Nucleotide or protein query sequences against the specified database using the BLAST suite of algorithms. GenBank nucleotide records are located in separate databases that must be searched independently.
• Network Entrez is a client/server version9

Where in the data chain could this tool be used?

• User’s machine

When could this tool be used?

• At the time of a user request

Availability

• GenBank: http://www.ncbi.nlm.nih.gov/Genbank/
• Entrez search: http://www.ncbi.nlm.nih.gov/Entrez/
• PubMed publications: http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed

• Submission guide: http://www.ncbi.nlm.nih.gov/Genbank/submit.html
• NCBI National Center for Biotechnology Information: http://www.ncbi.nlm.nih.gov/
• Active development. Release 163. December 2007
• Restrictions: no restrictions on the use or distribution of the GenBank data.10

Comments

GenBank accepts all DNA sequences. As a consequence of this policy, some of the sequences here are rubbish. Compare this to BOLD which only accepts sequences from the 5' region of the mitochondrial gene COI.