NCBI Blastn+ command line - How do I limit to a specific TSA project or organism?

Question

[elesbb91]

I am usign blastn+ to do some batch processes and to go through the tsa_nt database. However, I need to limit to specific taxids. If I use taxids parameter I am told that taxids do not work on blast databases v4. But I need to limit the search to either a TSA project, or the specific organism. How can I do such a thing?

Answer 1

[GenoMax]

NCBI is supposed to switch to v5 version of blast database (New layout for NCBI BLAST FTP database site starting February 4, 2020 ) as default some time this week. So if you wait a few days you should have the tsa_nt database in v5 format.

EDIT: NCBI has made the change to BLAST+ FTP site. Looks like tsa_nt is not included in today's release of V5 databases. Perhaps later in the week.

[elesbb91]

Well that is an easy solution!! Thanks so much!