[Bioperl-l] How to get more results from Blast

Scott Markel SMarkel at accelrys.com
Wed Nov 12 16:45:52 EST 2008


The BLAST command line options are "-b" (number of alignments)
and "-v" (number of hits).  The defaults are 250 and 500,
respectively.  You probably want to set them to the same value,
otherwise you'll get hits in the one-line summary with no
corresponding pairwise alignment.


Scott Markel, Ph.D.
Principal Bioinformatics Architect  email:  smarkel at accelrys.com
Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
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> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sean ohEigeartaigh
> Sent: Wednesday, 12 November 2008 8:33 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] How to get more results from Blast
> Hi, I'm using the module Bio::Tools::Run::StandAloneBlast.
> The standard cutoff for Blast to display a sequence comparison appears to
> be 250 results. How do I adjust this parameter to increase the cutoff to,
> say, 1000 results? I need to be able to look at Blast results in a lot of
> depth.
> Thanks very much for your help,
> Sean O hEigeartaigh.
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