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

[Steve Chervitz]

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.

Steve A. Chervitz                  
http://genome-www.stanford.edu/perlOOP/bioperl/blast/

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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