Bioperl: is there a $hit->db method in Blast module?
email@example.com (Steve A. Chervitz)
Mon, 16 Nov 1998 13:36:16 -0800 (PST)
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 = $hit->name();
If there are multiple identifiers, as in your example, they will be
supplied as "P52607/FLII_BORBU".
This is not as well-documented as it should be. Apologies for the
confusion. There are a few issues with the handling of identifiers
that will be addressed with the next release.
Steve A. Chervitz
Catherine Letondal writes:
> I am using Blast module version 0.062.
> I know that there is a method to get the name ($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 -- firstname.lastname@example.org -- +33 (1) 40 61 31 91
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