software to check the primer dimer
Posted 09 November 2004 - 04:12 PM
Posted 09 November 2004 - 06:44 PM
So I would suggest for each region you want to study you design at least two separate pairs of primer just in case someone won't work.
There are programs that check the quality of your primers but only experiment will tell if your primers work or not.
In your another post, you said your negative controls show band bigger than your expected product. First make such it is not a contamination. I think it is unlikely primer dimer amplification.
Personally, I have used the program to design primers for some time and have hardly got primers that didn't work. Before that, I designed primers manually at whatever places that are convenient in terms of meeting the rules of bisulfite PCR and also got pimers that worked for the most of the time. So I would say for bisulfit PCR, the first rules to follow are those set by bisulfite PCR, then follow the rules used by regular PCR. If the second set of rules cannot be satisfied and there is no other better place for primer, just go ahead and test your primers by PCR.
Posted 10 November 2004 - 09:15 AM
I really appreciate your help. But I still have another question.
When you use methprimer, did you choose the option of "CpG island prediction"? Or just use the option "Pick MSP primers"? Is the default parameter for the "CpG island prediction" ok?