program for checking primer pairs' uniqueness

[shuang]

Please suggest a software which can check multiple primer pairs' uniqueness.

I use Bowtie to check multiple primers's uniqueness. I want to further to check if each input primer pair can amply a unique fragment. The ref template is a genome.

[swbarnes2]

Bowtie doesn't seem like a bad idea. But in silico PCR is the term you are looking for. If your genome is on UCSC, you can do it there.

http://genome.ucsc.edu/cgi-bin/hgPcr?command=start

You might fine a higher throughput solution here

http://biostar.stackexchange.com/questions/10212/in-silico-pcr-assay

I've done it on modest number of pairs (a few dozen) by writing a little perl script that submitted the pairs one at a time to the ucsc site, but I don't know if that's considered proper if you have a very large number.