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Submitting Third Party Annotation Records Using Standard Submission Tools
The Third Party Annotation (TPA) database allows researchers to submit records that provide additional biological annotation but are based on existing records in GenBank. As pointed out in the recent NCBI News (Vol. 15, issue 1) these TPA records can now include a wider range of submission types including inferential findings. This article explains how to submit these TPA records to NCBI through the two standard GenBank direct submission tools, BankIt and Sequin. Before beginning either submission route, one or more sequences from one of the collaborating nucleotide sequence databases, DDBJ, EMBL, or GenBank must be identified as the source data for the TPA record. TPA records cannot be based on Reference Sequences or other non-primary sequence data. All TPA annotations must have some direct or indirect experimental support. The acceptable kinds of experimental evidence are described on the TPA submissions page.
Submitting TPA Records Using BankIt
The popular Web submission tool BankIt provides a simple interface for direct submission to GenBank and also allows submission to the TPA database.
Submitting TPA Records Using Sequin
The stand-alone submission and annotation tool, Sequin, also allows submission of TPA records. Sequin provides a powerful platform for propagating features across large and complicated sets of data and saves time and effort for batches or large records. The Sequin Homepage provides more information on downloading and using the Sequin program.
Begin a GenBank or TPA submission with Sequin by clicking the "Start New Submission" button on the main window of the program. Enter contact and author information and navigate through the dialog windows using the "Next" and "Previous" buttons as usual. Select the radio button for "Third Party Annotation" on the "Sequence Format" dialog window. Enter a description of the biological experiments used as evidence for the TPA in the "TPA Evidence" dialog window prompts. After importing the sequence(s) and adding remaining features, enter the DDBJ/EMBL/ GenBank accession number(s) used in the as data sources in the columns on the "Assembly Tracking" dialog. Like the BankIt submission, the preliminary flatfile view in Sequin will show the temporary COMMENT field that indicates that the submission is to the TPA database and lists the primary accession number. Send the completed Sequin TPA submission in an e-mail to
TPA records that have been submitted to NCBI using BankIt or Sequin are released into the NCBI public databases once the TPA data is published in a peer-reviewed journal. At NCBI, TPA records are a part of the sequence databases available for searching through the Entrez and the BLAST services.