A few monthes ago, I wrote a tool to find the best strategy for PCR in multiplex condition. The program takes as input a set of valid pairs of PCR primers for a set of targets and it builds the content of the PCR (a mix of primer), it finds how to pool the PCR in a gel in order to get distinct fragments. Some parameters are:
- -m maximum number of fragments per dye
- -D minimal distance between two fragments in a gel.
- -T maximal difference of temperature in a PCR.
- -c maximal number of PCR in a dye
- -g maximal number of pair in PCR.
- -f number of dyes
This software was created for a project that was canceled so I don't know if my algorithm works. I'm looking for people needing to peek primers for multiplex PCR in order to test my program (and write a paper if it works !...). Best would be someone on the Evry Genopole or near Paris.