10/05/12: How to Design Primers and Probes for Almost Any qPCR/PCR Target
My advice is to use IDT’s PrimerQuest.
I have been working with some customers in Denmark to help get them started on this, because they are studying organisms that are not included in the (pretty big) model organism defaults to be found in IDT’s other design tools (SciTools).
PrimerQuest is pretty easy to use and I’ve posted a very short “how to” guide here. The only time-consuming part of using this tool is the BLAST you need to do on the primers/probes, but come on, if you’re in research isn’t that your job?