[Bioperl-l] Bioperl-l Digest, Vol 57, Issue 10

Susan J. Miller sjmiller at email.arizona.edu
Tue Feb 5 15:23:28 EST 2008


bioperl-l-request at lists.open-bio.org wrote:
>
> Message: 2
> Date: Thu, 31 Jan 2008 10:34:31 +0100
> From: Georg Otto <georg.otto at tuebingen.mpg.de>
> Subject: Re: [Bioperl-l] Bio::DB::GenBank and large number of requests
> To: bioperl-l at bioperl.org
> Message-ID: <m1lk66uymw.fsf at tuebingen.mpg.de>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi,
> 
> I succeeded with a similar task using the seqhound database. I had a
> list of > 200,000 gid numbers, but I guess it can work in a similar
> fashion using accession numbers. 

Hi Georg,

How recently have you used the SeqHound database?  We installed it from 
CPAN but when we try to run the following test script this error occurs:

MSG: HTTP::Request error: 500 Can't connect to seqhound.blueprint.org:80 
(Bad hostname 'seqhound.blueprint.org')

Script:
#!/usr/local/bin/perl
use warnings;
use Bio::SeqIO;
use Bio::DB::SeqHound;

my $sh = Bio::DB::SeqHound->new();
my $seq = $sh->get_Seq_by_acc("CAA28783");
print $seq->display_name, "\n";


Do you know if SeqHound has moved?  Is there a way to comfigure it so 
that it works?

Thanks,
-susan

Susan J. Miller
Manager, Scientific Data Analysis
Biotechnology Computing Facility
Arizona Research Laboratories
(520) 626-2597


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