On Tue, Feb 8, 2011 at 3:46 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> Hello Peter,
> If these are standard length PCR primers, then UCSC's In-Silico PCR tool
> would be an option. It is a varient of BLAT and the source is available from
> Kent Informatics. Here is a UCSC link to the online version (send Jim Kent
> an email for a copy):
> http://genome.ucsc.edu/cgi-bin/hgPcr?command=start
> A wrapper could be made for your own instance or just use it command-line
> before loading data. If this is not what you had in mind, please let us
> know,
> Best,
> Jen

Thanks Jen,

If I've understood the purpose of the UCSC's In-Silico PCR tool it is for
predicting the PCR product of a given primer pair and genome sequence.
That's now quite what I have in mind - more like EMBOSS' primersearch
- but I'm sure would be useful at some point.

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