[Bioperl-l] parse Blast Output and Composition Based Statisticsparameter

[Barry Moore]

Hubert,

What exactly isn't working for you with the composition based
statistics.  Are you getting different e-values from Bioperl vs. NCBI
website.  It seems to be working OK for me (at least on one quick test).

Barry

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of Jason Stajich
> Sent: Monday, January 16, 2006 6:12 PM
> To: bioperl-ml List
> Cc: Hubert Prielinger
> Subject: Fwd: [Bioperl-l] parse Blast Output and Composition Based
> Statisticsparameter
> 
> sorry - i don't really have the time to support this module - lots of
> people on the list use it so they can hopefully help.
> 
> Begin forwarded message:
> 
> > From: Hubert Prielinger <hubert.prielinger at gmx.at>
> > Date: January 16, 2006 3:45:21 PM EST
> > To: Jason Stajich <jason.stajich at duke.edu>
> > Subject: Re: [Bioperl-l] parse Blast Output and Composition Based
> > Statistics parameter
> >
> > Jason Stajich wrote:
> >
> >> (please don't try and post to bioperl-announce, it is not for
> >> questions.)
> >>
> >> On Jan 12, 2006, at 6:57 PM, Hubert Prielinger wrote:
> >>
> >>> Hello,
> >>> I want to know, if there is a possibility to get from a Blast
> >>> Outputfile the whole Sequence of a protein not only the best
> >>> local  alignment...
> >>> for example:
> >>>
> >> No. The parser can only return to you what is in the report file...
> >> use Bio::DB::GenPept to retrieve the sequence via the web or
> >> (recommended) use a locally indexed sequence database like
> >> Bio::DB::Fasta
> >>
> >>> >ref|XP_480077.1| hypothetical protein [Oryza sativa (japonica
> >>> cultivar-group)]
> >>> dbj|BAD33542.1| hypothetical protein [Oryza sativa (japonica
> >>> cultivar-group)]
> >>>         Length=95
> >>>
> >>> Score = 24.1 bits (47),  Expect =   493
> >>> Identities = 6/7 (85%), Positives = 7/7 (100%), Gaps = 0/7 (0%)
> >>>
> >>> Query  2   KKRRRWW  8
> >>>                K+RRRWW
> >>> Sbjct  87  KRRRRWW  93
> >>>
> >>> and now, if I parse the file, I want to get the whole Sequence
> >>> of  this hypothetical protein....is that possible with hsp for
> >>> example,  or any other way....
> >>>
> >>> my second question is:
> >>> I do my blast search with bioperl and the remoteblast
> >>> module.....each parameter is working very well, except the
> >>> composition based statistics parameter....
> >>> it looks like that:
> >>>
> >>> my $factory = $Bio::Tools::Run::RemoteBlast::HEADER
> >>> {'COMPOSITION_BASED_STATISTICS'} = 'yes';
> >>>
> >> uh no that is not how you would do it.
> >> You can make it the default for any factories you use in the
> >> script  by doing this
> >>
> >>> $Bio::Tools::Run::RemoteBlast::HEADER
> >>> {'COMPOSITION_BASED_STATISTICS'} = 'yes';
> >>
> >> then
> >> $factory = Bio::Tools::Run::RemoteBlast->new();
> >>
> >>
> >>  =OR=
> >> Once you have a factory object you can set the parameter
explicitly:
> >> $factory->submit_parameter('COMPOSITION_BASED_STATISTICS', 'yes');
> >>
> >>> it should work like that, but it doesn't....
> >>>
> >>> Thanks for your help in advance......
> >>>
> >>> regards
> >>> Hubert
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at portal.open-bio.org
> >>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> >> --
> >> Jason Stajich
> >> Duke University
> >> http://www.duke.edu/~jes12
> >>
> >>
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at portal.open-bio.org
> >> http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >>
> > Hi Jason,
> > I have tried everything that you suggested, but the Composition
> > Based Statistic parameter isn't still working, every
> > other parameter works using e.g
> >
> > $Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = '1000';
> >
> > thanks in advance
> > Hubert
> >
> 
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
> 
> 
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