Blast plus command line filter !
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6.4 years ago
empyrean999 ▴ 180

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 • 3.1k views
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6.4 years ago
arnstrm ★ 1.8k

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.

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

 

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thank you. i will look in to that

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