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

Lincoln Stein lstein at cshl.edu
Mon Jul 12 10:04:45 EDT 2004

Bio::DB::GenBank and Bio::DB::GenPept use the approved batch mode 
retrieval.  There is, however, a caveat, which is that NCBI will 
arbitrarily truncate the number of sequences you can retrieve at 
periods of high load.  Recent CVS versions of bioperl will restart 
the fetch if this happens, but I recommend that you limit your 
requests to periods outside the 1-6 pm EST period of high activity.


On Monday 12 July 2004 12:27 am, Chris Fields wrote:
> 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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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

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