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Article #2626Re: blast command - one hit is sufficient
From: darked
Date: Tue, 01 Apr 2008 20:20
Date: Tue, 01 Apr 2008 20:20
41 lines
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3391 bytes
On 31 Mar, 16:49, martin.burk...@gmail.com wrote: > 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 I do not think that you can change the default behavior of blast (== look for all matches) without digging into C-code of the program. There is no program switch to do so. You may restrict the output with '-v 1' switch: Number of database sequences to show one-line descriptions for (V) [Integer] If you badly need to run it a bit faster you may chek the alternative blast implementations: http://openwetware.org/wiki/Wikiomics:BLAST_tutorial#BLAST_implementations darked http://openwetware.org/wiki/Wikiomics:Bioinfo_tutorial
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