[Bioperl-l] another searchIO bug? with blast report
Chris Fields
cjfields at uiuc.edu
Tue Feb 21 17:30:58 UTC 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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