[Bioperl-l] BLAST running options

[Chris Fields]

There were some posts about this a few months back.

http://bioperl.org/pipermail/bioperl-l/2006-April/021341.html

Essentially, most responders suggested not using BLAST, but I believe  
there were a few who gave pointers.

Chris

On Jul 8, 2006, at 3:59 PM, Vesselin Baev wrote:

> Hi,
> I'm parsing Blast results, but I need an Blast option to limit  
> limit and
> decrease the Blast number of results.
> I'm blasting an oligo about 40nt and I need only results which are  
> with
> mismatches (not more than 10) or exactly matching but in the length as
> the query - 40.
> I do not want all the big amount of results that blast gave me about
> shorter matching.
>
> Do anyone knows what king of BLAST option to use?
> Thanks
>
> -- 
> ------------------------------------------------
>
> University of Plovdiv
> Faculty of Biology
> Dept. Molecular Biology and Plant Physiology
> Tzar Asen 24
> Plovdiv 4000, BULGARIA
> vebaev at gmail.com
> tel.00359889034044
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign