[Bioperl-l] Batch Entrez with Bio::DB:GenBank or Bio::DB:GenPept

Brian Osborne brian_osborne at cognia.com
Mon Jul 12 09:21:27 EDT 2004


Yes, get_stream_by_Acc already does this.

my $db = Bio::DB::GenBank->new;
my $seqio = $db->get_Stream_by_acc(["M12345","AB123456"]);
while (my $seq = $seqio->next_seq){

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 Chris Fields
Sent: Monday, July 12, 2004 12:28 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] Batch Entrez with Bio::DB:GenBank or Bio::DB:GenPept

Is there a way to use Batch Entrez via Bio::DB::GenBank or
Bio::DB::GenPept, or does get_Stream_by_acc() or similar methods
automatically retrieve in batch mode?  I want to retrieve ~1500-2000
protein sequences from GenBank, and I couldn't find a clear-cut way for
specifically asking for a batch retrieval.  Or do you recommend using
the Entrez web interface directly?

Chris Fields
Postdoctoral Reseacher - Dept. of Biochemistry
Laboratory of Dr. Robert Switzer
University of Illinois at Urbana-Champaign

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