Bioperl: is there a $hit->db method in Blast module?
Tue, 17 Nov 1998 12:25:04 +0100
Steve Chervitz writes:
> 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 -- firstname.lastname@example.org -- +33 (1) 40 61 31 91
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