Bioperl: is there a $hit->db method in Blast module?

[Ewan Birney]

Catherine - 

I am sure bioperl is really interested in the script (!) we
have a special 'script central' for these sorts of things.

If you send the script to me I'll persuade chris dadigan to
find some place for it on bio.perl.org

Did you install all of bioperl-0.03? Any glitches?



On Tue, 17 Nov 1998, Catherine Letondal wrote:

> 
> Steve Chervitz writes:
> > Catherine,
> > 
> > The database for the hit (subject) sequence can be obtained using the
> > database() method on the hit object:
> > 
> >    $db = $hit->database();
> > 
> > The database identifier can be obtained using the name() method, which 
> > is inherited from Bio::Root::Object.pm.
> > 
> >    $id = $hit->name();
> > 
> > If there are multiple identifiers, as in your example, they will be
> > supplied as "P52607/FLII_BORBU". 
> > 
> > This is not as well-documented as it should be. Apologies for the
> > confusion. There are a few issues with the handling of identifiers
> > that will be addressed with the next release.
> 
> Thanks. I have put a perl script using this feature as "sequence/entry extractor"
> from a Blast run by the Web (http://bioweb.pasteur.fr/seqanal/blast/intro-uk.html)
> (and directly : http://www-bioweb.pasteur.fr/seqanal/interfaces/seqsblast.html)
> 
> The script is very simple, but if someone is interested, I can put it somewhere.
> 
> > Catherine Letondal writes:
> >  > 
> >  > Hi,
> >  > 
> >  > I am using Blast module version 0.062.
> >  > 
> >  > I know that there is a method to get the name ($hit->name) of the subject
> >  > sequence, but is it possible to get the database "name" of the subject 
> >  > as it appears in the HSP list of blast reports:
> >  > 
> >  > sp|P52607|FLII_BORBU FLAGELLUM-SPECIFIC ATP SYNTHASE (EC 3.6.1....    27   0.84
> >  > 
> >  > In this example, the "sp" string could be useful to fetch the entire entry from 
> >  > the corresponding sequence database (Swissprot), not only the HSP part of this sequence 
> >  > with the $hsp->seq_str('sbjct')).
> >  > 
> >  > Thanks in advance,
> >  > 
> 
> --
> Catherine Letondal -- letondal@pasteur.fr -- +33 (1) 40 61 31 91
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Ewan Birney
<birney@sanger.ac.uk>
http://www.sanger.ac.uk/Users/birney/

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