[Bioperl-l] search by keyword

[Brian Osborne]

Alisha,

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:

 http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html


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
Holloway
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
-- 
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
530-752-1449 Fax
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