[Biopython] Is there any in silico PCR tool on biopython?

[Sean Davis]

On Wed, Dec 16, 2009 at 12:08 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Wed, Dec 16, 2009 at 4:57 PM, Carlos Javier Borroto
> <carlos.borroto at gmail.com> wrote:
>> Hi there,
>>
>> I'm looking for a way to show some information on the specificity of
>> sets of primers I'm designing, I'll love to have a way to run an in
>> silico PCR reaction and parse the results with biopython.
>>
>> Is there something to use with one of the available PCR simulation tools?
>>
>
> I know people use Biopython with primer3 (usually the EMBOSS
> wrapped version, eprimer3).

Carlos,

If it is something like the UCSC genome browser in-silico PCR (for
mapping the putative amplimers from a set of primers), they (UCSC)
have an executable of the software.  I always have trouble finding
their software tools, but they are very responsive to email if you
have problems.  I don't have an example output file, but I bet it is
just tab-delimited text, so parsing is probably not too difficult.

Sean