[Bioperl-l] another searchIO bug? with blast report

Chris Fields cjfields at uiuc.edu
Tue Feb 21 12:30:58 EST 2006


Anders,

I think you should look through the mail list archives for an answer,
specifically:

http://portal.open-bio.org/pipermail/bioperl-l/2004-November/017285.html

Look up the other methods in Bio::Search::HSP::BlastHSP as well. They may be
more helpful.  I can't help but think there is something wrong with the
logic in your subroutines since they don't call other methods built in to
HSP objects.  It may be an off-by-one error.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign 


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Anders Stegmann
> Sent: Friday, February 17, 2006 3:18 AM
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] another searchIO bug? with blast report
> 
> 
> 
> >>>Anders Stegmann <anst at kvl.dk> 02/16/06 11:20 am >>>
> Hi!
> 
> I am blasting a protein seq (query) against an identical seq with a
> deletion of Aa nr 61 (subject).
> Then I print out the type of nomatch Aa and its position.
> The nomatch for the query seq is Aa G at position 61, which is correct.
> The nomatch for the subject seq is V at position 60, which is definitely
> not correct!?
> 
> Is this a bug?
> 
> testblast2.pl is the program to run
> 
> Q0045 is the query seq.
> 
> Q0045del61 is the subject seq (it has to be formated: formatdb -i
> Q0045del61 -p T -o F).
> 
> Regards Anders.
> 




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