[Bioperl-l] Specifying the search set in NCBI BLAST

Cook, Malcolm MEC at stowers.org
Fri Oct 22 11:40:24 EDT 2010


I agree with Dave.

But, if you must use BioPerl, see http://doc.bioperl.org/releases/bioperl-1.4/Bio/Tools/Run/RemoteBlast.html where it shows this code:

 $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';

You'll probably want to set your database to  est_others (c.f. http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/remote_blastdblist.html#2 )

--Malcolm
 

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Dave Messina
Sent: Friday, October 22, 2010 10:30 AM
To: Iago Lowe
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Specifying the search set in NCBI BLAST

Hi Iago,

It is possible to do this with BioPerl, but I would recommend simply downloading Blast+ (note the +) and using the -entrez_query and -remote options.

Dave


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