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.

www.ncbi.nlm.nih.gov/Genbank/TPA.html

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.

www.ncbi.nlm.nih.gov/BankIt

As with GenBank submissions, the BankIt TPA submission route is best for simple submissions of small numbers of records. The Sequin submission route, described below, is a better choice for large or complicated TPA submissions. To submit a TPA record using BankIt, begin as usual by entering the length of the sequence and pressing the "New" button under "GenBank Submissions by WWW" section of the BankIt page. This launches the Bankit Web submissions form that is normally used to prepare GenBank submissions. To specify a TPA submission, set the radio button to "No" to answer the questions on the form: "Is This Primary Sequence Data? Have you determined and annotated the sequence you are submitting?". Follow the instructions on the form and enter the DDBJ/EMBL/ GenBank accession numbers of source data and a concise description of the supporting experimental evidence for the biological annotation in the specified text areas. The rest of the submission process is the same as that for standard GenBank data. Once the submission process is complete, the preliminary flatfile view reports, in a temporary COMMENT field, that this is a record from the third party annotation database and lists the primary database accession numbers of the source data. The COMMENT will be removed as the record is processed by the submission staff at NCBI. The BankIt acknowledgement message returned by e-mail, contains the interim BankIt number, designates the submission as a TPA, and includes the accessions and concise evidence information.

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.

www.ncbi.nlm.nih.gov/Sequin

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

gb-sub@ncbi.nlm.nih.gov

to complete the submission process.

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.
—MR