This is a test version of Biostars. For the public version, visit https://www.biostars.org.
NCBI Blastn+ command line - How do I limit to a specific TSA project or organism?

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?

ncbi assembly
• 1,383 views • link
updated by GenoMax GenoMax • written by elesbb91 • elesbb91

1 answer

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.

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by elesbb91 • elesbb91

Log in to answer this question.

More posts like this