[Bioperl-l] Bio::Tools::Run::Primer3 vs Web Primer 3

armendarez77 at hotmail.com armendarez77 at hotmail.com
Mon Jun 7 14:27:33 EDT 2010


Hello again,

We just upgraded to BioPerl 1.6.1 (from 1.6.0), but neither Bio::Tools::Primer3Redux or Bio::Tools::Run::Primer3Redux were included in the modules.  We looked at CPAN, but they weren't found their either.  From where can we download these modules?

Thanks,

Veronica


> Subject: Re: [Bioperl-l] Bio::Tools::Run::Primer3 vs Web Primer 3
> From: cjfields at illinois.edu
> Date: Sat, 5 Jun 2010 07:34:34 -0500
> CC: armendarez77 at hotmail.com; bioperl-l at lists.open-bio.org
> To: David.Messina at sbc.su.se
> 
> Just to note, it's very likely the web version is running Primer3 v2.  The BioPerl wrapper for Primer3 only supports v1; I rewrote the wrapper and parser to support both versions.  It's called Bio::Tools::Primer3Redux and Bio::Tools::Run::Primer3Redux, and is present in bioperl-dev if anyone is interested.
> 
> chris
> 
> On Jun 4, 2010, at 7:16 PM, Dave Messina wrote:
> 
> > Hi Veronica,
> > 
> > Without having checked to be sure, my guess is that either the version of Primer3 on the website is different from the one you're running locally or the default parameters on the website are different from the default parameters when running via B::T::R::Primer3.
> > 
> > If you run Primer3 on your machine outside of BioPerl — that is, just on the command line directly — do you get the same results as on the website?
> > 
> > 
> > Dave
> > 
> > 
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> > Bioperl-l at lists.open-bio.org
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> 
 		 	   		  
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