[Bioperl-l] Retrive the sequences from Blast report

Sean Davis sdavis2 at mail.nih.gov
Wed Jul 28 20:46:29 EDT 2004


If you have something like (from Bio::Search::Hit::HitI documentation):

    my $searchio = new Bio::SearchIO(-format => 'blast', -file =>
    my $result = $searchio->next_result;
    my $hit    = $result->next_hit;

    $hit_name = $hit->name();

    $desc = $hit->description();

Depending on where you are getting your blast results, you can probably grab
the name, description, locus, or accession and use Bio::DB::Genbank to look
up the sequence.  See Bio::DB::GenBank for details.

----- Original Message -----
From: "Sun, Jian" <jsun at utdallas.edu>
To: <bioperl-l at bioperl.org>
Sent: Wednesday, July 28, 2004 5:16 PM
Subject: [Bioperl-l] Retrive the sequences from Blast report

> Dear Bioperl:
>     Does anybody could provide me some advice on how to get or retrive the
sequence from a Blast search report, which will be saved in a sequence file
and then used for Clustalw alignment?
> Any help will be appreciated
> Jian
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

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