[Bio-software] Re: blast command - one hit is sufficient

darked via bio-soft%40net.bio.net (by darek.kedra from gmail.com)
Tue Apr 1 15:20:28 EST 2008


On 31 Mar, 16:49, martin.burk... from 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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