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.
