[BioC] PCR Primer Design tools in BioC?

[Herve Pages]

Hi Caroline,

Caroline Johnston wrote:
> Hi,
> 
> Are there any bioconductor packages which provide tools for PCR primer
> design?

I don't know for the design. But for testing and validating a library of primers
(by simulating a PCR experiment), there is the matchProbePair function in the
Biostrings package.

Description:
     In the context of a computer-simulated PCR experiment, one wants
     to find the amplicons mapped to a given primer pair. The
     'matchProbePair' function can be used for this: given a forward
     and a reverse probe (i.e. the chromosome-specific sequences of the
     forward and reverse primers used for the experiment) and a target
     sequence (generally a chromosome sequence), the 'matchProbePair'
     function will return all the "theoretical amplicons" mapped to
     this probe pair.

Note that matchProbePair will only return the locations of the amplicons so,
in order to complete the validation process, some extra work is required to
map those locations to the features that you are targetting.

Cheers,
H.