Question: Blast plus command line filter !
0
gravatar for empyrean999
4.9 years ago by
empyrean999160
Canada
empyrean999160 wrote:

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

blast unix command line • 2.6k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 4.9 years ago by empyrean999160
2
gravatar for arnstrm
4.9 years ago by
arnstrm1.8k
Ames, IA
arnstrm1.8k wrote:

Check this older post about setting up masked database for BLAST (https://www.biostars.org/p/6528/#6532). 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.

ADD COMMENTlink modified 4.9 years ago • written 4.9 years ago by arnstrm1.8k

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

 

ADD REPLYlink written 4.9 years ago by h.mon29k

thank you. i will look in to that

ADD REPLYlink written 4.9 years ago by empyrean999160
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