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

[Catherine Letondal]

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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