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Submitting Barcode Data to GenBank

Submitting Barcode Data to GenBank. 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.

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Submitting Barcode Data to GenBank

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  1. Submitting Barcode Data to GenBank Ilene Mizrachi November 28, 2011 Informatics Workshop

  2. Requirements for Barcode Compliance • Taxonomic Identification • Specimen Voucher ID • Collection Locality • Collection Date • DNA Sequence • Raw Sequence Reads • Assembled Sequence • PCR primers

  3. 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

  4. 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

  5. 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

  6. 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

  7. Acknowledgements • Colleen Bolin • Vasuki Gobu • Kamen Todorov • Michael Fetchko • Susan Schafer

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