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

Nathan Haigh n.haigh at sheffield.ac.uk
Fri Jul 15 08:43:16 EDT 2005

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


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?







Nathan Haigh

Bioinformatics PostDoctoral Research Associate


Room B2 211

Department of Animal and Plant Sciences

University of Sheffield

Western Bank


S10 2TN


Tel: +44 (0)114 22 20112

Mob: +44 (0)7742 533 569

Fax: +44 (0)114 22 20002


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