[Bioperl-l] Bio:Tools::Primer3, Bio::Seq::PrimedSeq, and Bio::SeqFeature::Primer

[Jason Stajich]

On Mon, 31 Mar 2003, Rob Edwards wrote:

> Hi all,
>
> I have split Primer3 into Bio::Tools::Primer3 to parse Primer3 output and
> Bio::Tools::Run::Primer3 to run primer3, including adding the in OK_FIELD and
> AUTOLOAD methods as suggested by others.
>
Good stuff Rob.

ChadM should weigh in too at some point I hope.

> Is there a way in Bio::Tools::Run::WrapperBase or Bio::Root::IO (or
> elsewhere?) to deal with creating a filehandle to print results out to? I
> couldn't find either a method or another implementation that has done this.
>

$self->_print will either print to STDOUT or if a requested filehandle
(-fh) or new file (-file => ">filename") is supplied upon object
initialization.

> Also, I added a Bio::Tools::ePCR module that will return a Bio::Seq object
> when given a template and two sequences to act as primers. (I am not sure
> about the name at the moment, and am happy to change it as NCBI has an ePCR
> program that doesn't do anything like this).
>
Name should change - there already is a Bio::Tools::EPCR which takes the
output from ePCR and turns it into Bioperl SeqFeatures so that one can
annotate genomic sequence with marker locations.

-jason
> http://www.salmonella.org/bioperl/primer3_v0.2.tgz
>
> I'd appreciate any feedback.
>
> Rob
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu