[Bioperl-l] 85% ATGCN

armendarez77 at hotmail.com armendarez77 at hotmail.com
Tue Jul 6 14:21:10 EDT 2010


Thank you.  The missing 'n' was the problem.  


Veronica



> From: cjfields at illinois.edu
> Date: Tue, 6 Jul 2010 12:17:03 -0500
> To: roy.chaudhuri at gmail.com
> CC: bioperl-l at lists.open-bio.org; bosborne11 at verizon.net; armendarez77 at hotmail.com
> Subject: Re: [Bioperl-l] 85% ATGCN
> 
> 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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