[Bioperl-l] 85% ATGCN

Roy Chaudhuri roy.chaudhuri at gmail.com
Tue Jul 6 12:31:04 EDT 2010


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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