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

[Chris Fields]

Thanks Brian and Lincoln!  Just wanted to clarify that.  I noticed that the 
documentation mentioned not spamming the NCBI server, so I did want to 
prevent that if possible.

Chris

At 09:04 AM 7/12/2004, Lincoln Stein wrote:
>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.
>
>Lincoln
>
>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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>--
>Lincoln D. Stein
>Cold Spring Harbor Laboratory
>1 Bungtown Road
>Cold Spring Harbor, NY 11724

__________________________________

Chris Fields - Postdoctoral Researcher
Lab of Dr. Robert Switzer

Address:

University of Illinois at Urbana-Champaign
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Phone : (217) 333-7098
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