[Bioperl-l] Get GIs from Taxonomy ID

Brian Osborne bosborne11 at verizon.net
Tue Jul 6 10:36:18 EDT 2010


Veronica,

Yes, when you're making your sequence object do something like:

-alphabet => 'dna'

For example:

use Bio::Seq;
 
$seq_obj = Bio::Seq->new(-seq => "aaaatgggggggggggccccgtt",
                         -alphabet => 'dna' );

Brian O.

On Jul 6, 2010, at 4:23 PM, <armendarez77 at hotmail.com> <armendarez77 at hotmail.com> wrote:

> 
> Hello,
> 
> I'm designing degenerate primers using
> Bio::Tools::Primer3 and Bio::Tools::Run::Primer3.  I'm allowing up to 3
> Ns, but on some sequences the script dies with the following error:
> 
> Sequence[AnGGACCAnGAGGCnGGAT] is less than 85% ATGCN, which doesn't look very DNA to me at Perl.pm line 629.  
> 
> 
> 
> I couldn't find any information on this error.  Is there a way to catch or override it?
> 
> Thank you,
> 
> Veronica 		 	   		  
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