Third PArty (TPA) Sequence

What is a Third PArty (TPA) Sequence?

A TPA Sequence is the assembly or reassembly of primary INSDC sequence data that has been subject to peer review. A TPA sequence is assembled from primary sequence data currently found in the DDBJ/EMBL/GenBank International Nucleotide Sequence Database. Feature annotation is not required to be part of the peer review for this TPA type. (Examples of such assemblies include complete viruses, mitochondria, or named biosynthetic gene clusters).

An example of a TPA:assembly is BK010317

As of January 2025, TPA-Exp and TPA-Inf submission types are no longer accepted as new submissions. Please see INSDC TPA Announcement for more information.

What is a primary sequence?

'Primary' sequences used to assemble a TPA sequence are those that have been experimentally determined and are now publicly available in the GenBank/EMBL/DDBJ databases, including SRA data (reported with their SRR numbers). They may not be from a proprietary database. Each primary sequence used to assemble a TPA sequence must be identified by a GenBank accession number in the TPA sequence submission. Assembly of SRA data that you generated is primary sequence data.

How Do TPA Sequence Records Differ from Other GenBank Records?

The display of a TPA sequence is similar to other GenBank/INSDC records, but includes the following:

• Keywords: TPA;THIRD PARTY ANNOTATION; TPA:assembly
• The label 'TPA_asm:'at the beginning of each Definition Line.
• A THIRD PARTY DATABASE Comment providing the Accession number(s) of the primary sequences that contribute to the TPA sequence

TPA sequence records are shared across INSDC and can be found using typical search methods in the GenBank database.

How to Submit TPA Sequence Data

Sequences must be submitted to the TPA database through the Submission Portal:

• On the 'Submission Type' input page, choose 'Third Party Assembly Data'.
• Later in submission, you will be prompted to provide a brief explanation of the evidence you have to support the new annotation/assembly you are presenting and the GenBank accession numbers of all primary sequences used to assemble your TPA sequence (for SRA data, provide the SRR accession numbers).
• Continue with the standard submission process. Be sure to add all new annotation for your TPA sequence on the 'Features' input page.
• The submission will be labeled as a TPA sequence and processed accordingly after it is successfully submitted.
• General Information
  • The entire submitted sequence must be covered by cited primary sequence data.
  • If sections of a sequence submitted to TPA have been newly determined by the submitter, those sequences (if they are more than 100 nt) must first be submitted to GenBank, processed, and released to the public before they can be cited as primary sequences

When are TPA sequences released?

• TPA sequences are held confidential until their accession numbers appear in a peer-reviewed publication in a biological journal.
• No sequence accepted for the TPA database will be released to the public until the submitter notifies GenBank of its publication or we determine independently that such information was published.
• When reporting that a TPA sequence's corresponding paper has been published, provide the DOI, PubMedID, or the URL of the journal's online paper

What should NOT be submitted to TPA

• Synthetic constructs such as cloning vectors that use well characterized, publicly available genes, promoters, or terminators; these should be submitted as primary data.
• Assembly of sequence data that you generated; these should be submitted as primary data
• Newly generated sequence that updates or changes existing sequence data from another submitter; these should be submitted as primary data
• Annotation only changes where the sequence is unchanged from the existing record
• Data that will not be submitted for publication in a peer-reviewed journal.
• Microsatellites, repeat regions, or single genes