[Bioperl-l] 85% ATGCN

armendarez77 at hotmail.com armendarez77 at hotmail.com
Tue Jul 6 11:58:11 EDT 2010


Hi Brian,

This sort of worked.  The script still dies with the same complaint when the primer sequence is 19 bases long and starts with an 'n':

Sequence [nGCnGTGCGTTGGTCnTTG]  is less than 85% ATGCN, which doesn't look very DNA to me at ....


However, other 19bp long sequences with 3 internal n's are allowed.  Is there another way to prevent the script from dying when it comes across these sequences or should I just not allow these sequences to be processed?

Thanks,

Veronica

Subject: Re: [Bioperl-l] Get GIs from Taxonomy ID
From: bosborne11 at verizon.net
Date: Tue, 6 Jul 2010 16:36:18 +0200
CC: bioperl-l at lists.open-bio.org
To: armendarez77 at hotmail.com



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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