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

Chris Fields cjfields at uiuc.edu
Fri Feb 17 14:17:32 EST 2006


No, haven't ignored it.  Just been busy going through SearchIO::blast again
(I've perltidy'd it) since BLASTN and TBLASTX output (v2.2.13) don't work;
looks like all others should.  Trying to fix one problem at a time.  I'll
look at this next.  Don't worry about it.  ;>

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 Jason Stajich
> Sent: Friday, February 17, 2006 1:02 PM
> To: Anders Stegmann
> Cc: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] another searchIO bug? with blast report
> 
> In case people on the list think that by my speaking up about
> question means they should ignore it...
> 
> Hopefully someone else can help debug this - I really don't have time
> I'm afraid.
> 
> -jason
> 
> 
> On Feb 17, 2006, at 4:18 AM, Anders Stegmann wrote:
> 
> >
> >
> >>>> 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.
> >
> >
> > <Q0045>
> > <Q0045del61>
> > <testblast2.pl>
> > <testigen1.html>
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> 
> 
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