[Bioperl-l] SeqHound

Chris Fields cjfields at uiuc.edu
Tue Feb 5 16:38:31 EST 2008


The URL has changed.  I'll fix this in bioperl-live.

You can fix this in your script directly for now (though I hate  
globals):

use Bio::DB::SeqHound;

$Bio::DB::SeqHound::HOSTBASE = 'http://dogboxonline.unleashedinformatics.com/' 
;

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

chris

On Feb 5, 2008, at 2:23 PM, Susan J. Miller wrote:

> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





More information about the Bioperl-l mailing list