primer software - (Jan/13/2010 )
I am having problems with a PCR, and now I was told that I should run the primers through primer 3 or another programm to check whether they strongly tend to build primer-dimers. I did check primer 3 but didnt find a tool for that, its more a creating primers tool. I did run it with my primers but as they are gateway primers they are too long, so I am having problems to use it...
so my question: does anyone know a good tool for those things or am I just too stupid to use primer 3?
The hairpin and primer-dimer tools at idtdna.com are quite good. Unfortunately, they fail to distinguish 3' from 5' overhangs. The 3' overhangs are relatively unimportant.
I am using a very simple primer design software, FastPCR, free to download and use, to design and test my primers.
Works well in my hand, been using it to design more than 200 pairs of primer.
link to download FastPCR http://www.biocenter.helsinki.fi/bi/Programs/fastpcr.htm