[Bioperl-l] 85% ATGCN

Chris Fields cjfields at illinois.edu
Tue Jul 6 13:17:03 EDT 2010


Yeah, surprised that one didn't show up before.  'use strict' and perl 5.12 for the win!

chris

On Jul 6, 2010, at 11:31 AM, Roy Chaudhuri wrote:

> Hi Veronica,
> 
> Fairly obviously this is a bug, since your sequence is 100% ACTGN. It looks like it has already been fixed by Chris Fields in a commit on May 20th:
> http://github.com/bioperl/bioperl-live/commit/7ea9c9d4a062d555efc51b98289a862395ec0664
> 
> So if you install bioperl-live from GitHub (http://github.com/bioperl/bioperl-live/tarball/master) it should fix your problem. Or you could just correct the offending tr statement in your installed Bio/Perl.pm file in the same way as the above commit.
> 
> Cheers.
> Roy.
> 
> 
> 
> On 06/07/2010 16:58, armendarez77 at hotmail.com wrote:
>> 
>> 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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