dr ilene mizrachi - genbank barstool
DESCRIPTION
The process of submitting barcode data to GenBank, using the BarSToolTRANSCRIPT
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USANational Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
Ilene MizrachiNovember 28, 2011
Informatics Workshop
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
Requirements for Barcode Compliance
Taxonomic IdentificationSpecimen Voucher IDCollection LocalityCollection DateDNA Sequence
Raw Sequence ReadsAssembled Sequence
PCR primers
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
Submission ToolsBarcode Submission Tool - web-based wizard
http://www.ncbi.nlm.nih.gov/WebSub/index.cgi?tool=barcode
BankIttbl2asn –command line tool with Barcode
validationSequin – downloadable application with
interactive wizards
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
Files required for submissionfasta-formatted nucleotide sequence with
[organism=] in the definition linefasta-formatted protein sequence (optional)Source modifiers (collection_date,
collected_by, specimen_voucher)Trace information fileTrace archive file
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
QA checks in GenBankBarcode data element complianceSequence alignment to detect reading frame
shiftsCoding regions translate without internal stop
codonsReported latitude-longitude falls within
reported country
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
UpdatesSubmitter 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: [email protected]
National Center for Biotechnology Information – National Library of Medicine – Bethesda MD 20892 USA
AcknowledgementsColleen BolinVasuki GobuKamen Todorov
Michael FetchkoSusan Schafer