GenBank

GenBank

• Annotated collection of all publicly available nucleotide and protein sequences
  
  • Built and managed by the NIH National Center for Biotechnology Information (NCBI)
    • A division of the NAtional Library of Medicine (NLM)
      
  • Sequences are contributed by investigators
    
    • Automated formatting with Sequin
      
  • Predicted amino acid sequences are most often derived from DNA sequences rather than from protein sequencing
    
• Part of the International Nucleotide Sequence Database Collaboration
  
  • DNA Database of Japan (DDBJ)
    
  • European Molecular Biology Laboratory (EMBL)
    
• Scope
  • Release 102 (August 1997) had 1 billion nucleotide bases
    
  • Size double every 15 months
    
  • ~70% of sequences are ESTs
    
  • 30,000 species are represented (~55% of the database in human)
    
  • New release issued every 2 months (by FTP from the NCBI site)
    
  • Daily updates are obtainable (by FTP from the NCBI site)
    

• Database items are contained in a flatfile

GenBank file

• Header
  
  • Locus
    
    • Unique identifier
      
    • Now an accession number rather than a description
      
  • Length of sequence (50 bp to 350,000 bp)
    
  • Molecule type (DNA,RNA)
    
  • Division code (EST, STS, GSS, HGT, CON, etc.)
    
  • Definition of a cDNA sequence
    
    • Genus-species-product name (symbol) mRNA, complete cds.
      
    • Should describe the biology and source
      
    • VERY important-seen as description in search results
      
  • Accession number
    
    • Permanent sequence identifier
      
    • Cited in publications
      
    • Stays the same, even if sequence is changed
      
  • NID (gi, geninfo identifier number)
    
    • Identifies the exact sequence, changes with sequence change
      
  • Accession.version
    
    • A new substitute for Accession.gi, incremented by 1 with change
      
  • Keywords
    
    • Not common in modern submissions
      
  • Source line
    
    • Common or scientific name
      
  • Reference
    
    • Can be unpublished
      
    • Should have Medline and Pubmed identifiers
      
  • Credits
    
    • Names and mailing address
      

• Feature table
  
  • A series of annotations that describe the sequence and its features
    
  • Source
    
    • /organism qualifier indicates Genus and (sub)species
      
    • /map indicates chromosome mapping data
      
    • /tissue_type, /strain, and /dev_stage indicate tissue source
      
    • Clone identification (library type, clone name)
      
  • Gene, mRNA, intron, exon and Sig_peptide qualifiers
    
    • Indicate the DNA sequence number where these features begin and end
      
  • CDS
    
    • Defines the coding sequence beginning and ending DNA sequence number
      
    • Defines coding portions of exons in gene sequences
      
    • Contains database cross-references (protein ID,PID) to protein databases
      
    • Includes a full translation of CDS
      
• RNA
  
  • Can be used to define RNA features
    
• Misc_feature
  
  • Can be used to define domains or important elements
• Base count
  
  • Number of A,C,G,T in sequence