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

peter.d.ashton from googlemail.com via bio-soft%40net.bio.net (by peter.d.ashton from googlemail.com)
Tue Apr 1 05:29:54 EST 2008


On Mar 31, 4:49 pm, 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
>

Hi

if you add -v 1 -b 1 to your command line, blastall should only report
one hit, whichever output format (-m) you choose.

Cheers
pete

> (using blastall 2.2.15)
>
> Thank you :-)
> Martin




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