[Bioperl-l] Bio::Graphics and primer3 pipeline

[Nathan Haigh]

I'm creating a pipeline for passing around 200 sequences to primer3 in order
to generate primers. I want to be able to use Bio::Graphics to create a png
file for each sequence with the position of the primers shown and some of
the details about each primer (e.g. Tm, %GC).

 

Here's what I have so far in pseudocode:

 

Foreach Bio::Seq object

    Add position of introns as Bio::SeqFeature::Generic features

    Run Primer3 with Bio::Seq object

    Loop through primers, returning a Bio::Seq::PrimedSeq object

        Add primer as features using: Bio::Seq
object->add_SeqFeature(Bio::Seq::PrimedSeq);

 

Now create png using Bio::Graphics

 

This works ok, but I'm lost trying to get the Tm and GC content of the
primers as returned by Primer3

 

Does anyone have a script that can do something similar that I might try to
work out whats going on?

Thanks

Nathan

 

 

 

----------------------------------

Nathan Haigh

Bioinformatics PostDoctoral Research Associate

 

Room B2 211

Department of Animal and Plant Sciences

University of Sheffield

Western Bank

Sheffield

S10 2TN

 

Tel: +44 (0)114 22 20112

Mob: +44 (0)7742 533 569

Fax: +44 (0)114 22 20002