Blast plus command line filter !

Question

[empyrean999]

Hello All,

I am doing blast with "NR" database which is taking very long time and I am interested in searching only specific species. Is there a way to submit in the blast option to restrict it to search for specific species. I am using blast plus. In older blast there is command blastall -u "organism name". Is there any similar option in blast plus other than creating separate database from "NR".

Thanks

Answer 1

[arnstrm]

Check this older post about setting up masked database for BLAST (Vertebrate Subset Nr Database? Build My Own?). In short, you download GI list for the species you're interested, use blastdb_aliastool with the -gilist flag to create a restricted database, and use this database to blast your sequences.

[h.mon]

In addition, blast+ programs (blastn, blastp, etc) accept -gilist, -seqidlist or -negative_gilist to restrict the search to subsets of your database.

[empyrean999]

Thank you. I will look in to that