Dr Ilene Mizrachi - GenBank BarSTool

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

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Dr Ilene Mizrachi - GenBank BarSTool

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

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