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

[Rob Edwards]

Hi all,

I needed to design some primers with primer3, and as the current modules were 
outlines I took Chad Matsalla's work and built on it.

I have enhanced the three modules that were started:
Bio::Seq::PrimedSeq is a representation of a sequence with two primers 
attached.
Bio::SeqFeature::Primer is a single primer that can be associated with a 
sequence using PrimedSeq
Bio::Tools::Primer3 is a wrapper for the primer3 program 
(http://www-genome.wi.mit.edu/genome_software/other/primer3.html)

I spent most effort working on Primer3.pm which now will run primer3, as well 
as pass all the arguments you'd like (and perhaps some you wouldn't.....?) It 
will also return the results as raw feed, one primer at a time, or a stream 
of PrimedSeq objects that can be parsed out. The two example scripts 
demonstrate these at work.

There are some areas that are not truly bioperly yet, but I am working on it 
and gettting my way around it. At least the docs are complete.

Please take a look at these and see if they are worthy of including at some 
point in the future. All pointers as to what I should improve are appreciated.

The modules and scripts are available from 
http://www.salmonella.org/bioperl/primer_0.1.tgz Give them a try and see what 
you think!


Rob