Dr Ilene Mizrachi - GenBank BarSTool
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Dr Ilene Mizrachi - GenBank BarSTool

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The process of submitting barcode data to GenBank, using the BarSTool

The process of submitting barcode data to GenBank, using the BarSTool

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Dr Ilene Mizrachi - GenBank BarSTool Dr Ilene Mizrachi - GenBank BarSTool Presentation Transcript

  • Ilene Mizrachi November 28, 2011 Informatics Workshop
  • Requirements for Barcode Compliance
    • Taxonomic Identification
    • Specimen Voucher ID
    • Collection Locality
    • Collection Date
    • DNA Sequence
      • Raw Sequence Reads
      • Assembled Sequence
    • PCR primers
  • Submission Tools
    • Barcode Submission Tool - web-based wizard
      • http://www.ncbi.nlm.nih.gov/WebSub/index.cgi?tool=barcode
    • BankIt
    • tbl2asn –command line tool with Barcode validation
    • Sequin – downloadable application with interactive wizards
  •  
  • Files required for submission
    • fasta-formatted nucleotide sequence with [organism=] in the definition line
    • fasta-formatted protein sequence (optional)
    • Source modifiers (collection_date, collected_by, specimen_voucher)
    • Trace information file
    • Trace archive file
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  • QA checks in GenBank
      • Barcode data element compliance
      • Sequence alignment to detect reading frame shifts
      • Coding regions translate without internal stop codons
      • Reported latitude-longitude falls within reported country
  • Updates
    • Submitter may update GenBank records as new data becomes available including taxonomy, publication and sequence
    • Third parties may inform GenBank staff of publications or problems noted with sequence entries. Information will be passed on to the submitter.
    • Send to: update@ncbi.nlm.nih.gov
  • Acknowledgements
    • Colleen Bolin
    • Vasuki Gobu
    • Kamen Todorov
    • Michael Fetchko
    • Susan Schafer