[Bioperl-l] parse Blast Output and Composition Based Statistics parameter

[Jason Stajich]

(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
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--
Jason Stajich
Duke University
http://www.duke.edu/~jes12