[Bioperl-l] search by keyword

Brian Osborne brian_osborne at cognia.com
Sat Feb 5 17:30:41 EST 2005


Here is a code example:

use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;

$query = "Arabidopsis[ORGN] AND topoisomerase[TITL]";
$query_obj = Bio::DB::Query::GenBank->new(-db    => 'nucleotide',
                                               -query => $query );

$gb_obj = Bio::DB::GenBank->new;

$stream_obj = $gb_obj->get_Stream_by_query($query_obj);

while ($seq_obj = $stream_obj->next_seq) {
        # do something with the sequence object
     print $seq_obj->display_id, "\t", $seq_obj->length, "\n";

For information on fields:


Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Alisha
Sent: Thursday, February 03, 2005 2:32 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] search by keyword

I would like to search genbank using for sequences using a keyword 
(e.g. a CG number).  Which module would I use for this task?  I have 
found the modules for searching by accession number, ID, etc, but 
can't figure out how to search by keyword.

Many thanks in advance,

Alisha Holloway

Postdoctoral Fellow
Section of Evolution & Ecology
3347 Storer Hall
University of California
Davis, CA  95616

530-752-4253 Office
512-297-3958 Cell
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