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Article #2625blast command - one hit is sufficient
From: martin.burkert
Date: Mon, 31 Mar 2008 15:49
Date: Mon, 31 Mar 2008 15:49
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2589 bytes
Hello NG, i'm using command line blast for searching multiple nucleotide queries against a protein database. For each query I get a detailed output with hits on the database surviving my cutoff value. There can be a lot of hits for one single query. For my task it would be sufficient to know if there is any hit (below the cutoff) in the database for my query at all. Once the blast search was able to determine a hit which e-value is lower than my cutoff value it could print this hit to the output, stop searching and continue with the next query. Is some one out there, who can provide me with a simple solution using custom command line parameters for my blastall binary? That's my command until now: /blastall -p blastx -d /path/to/swissprot -e 1e-10 -i input.fas -m 9 > output.bla (using blastall 2.2.15) Thank you :-) Martin
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