Dr Ilene Mizrachi - GenBank BarSTool

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

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

Dr Ilene Mizrachi - GenBank BarSTool

by Consortium for the Barcode of Life (CBOL)

Accessibility

Categories

Upload Details

Usage Rights

Statistics

Dr Ilene Mizrachi - GenBank BarSTool Webinar Transcript