[Biopython] PCR primer dimers

[Brad Chapman]

Hi Ogan;

> Does any one know of a module in biopython that does primer 
> dimer/hairpin check. I scripted my own pcr primer tiling with a lame 
> dimer check function. It does a sliding search of self and cross 
> dimerization of primers but I know it is not the proper way.

My suggestion would be to use the primer3 program for primer design
problems. I've used it with a lot of success. Biopython has support 
using the eprimer3 commandline program from EMBOSS.  Here is some
rough code to get started with:

from Bio.Emboss.Applications import Primer3Commandline
from Bio.Emboss import Primer3
from Bio.Application import generic_run

cl = Primer3Commandline()
cl.set_parameter("-sequence", input_file)
cl.set_parameter("-outfile", output_file)
cl.set_parameter("-numreturn", 1)
generic_run(cl)

h = open(output_file, "r")
primer3_info = Primer3.read(h)
h.close()
# work with primer3_info record

Hope this helps,
Brad