How to run primer3 with mismatches and insertions?

Question

[test]

There are a lot of parameters in primer3. I can not find there how to find primer binding sites with primer3 with mismatches and insertions, but not exact match. Is it possible?

Answer 1

[Jean-Karim Heriche]

I don't think it's possible. Primer3 is designed primarily for PCR. Given a DNA template, primer3 selects PCR primers that minimize various constraints. Typically, mismatches and gaps lower quality of the primers so they are avoided. The only parameters that I can think of that deal specifically with mismatches are those related to secondary structure constraints. You should maybe rethink the problem you're trying to address. Are you trying to design primers for PCR or related approach (see values for parameter PRIMER_TASK) ? Then there may be other ways of specifying your constraints that using mismatches. For example, you could play with location of the primers using some combination of SEQUENCE_TARGET, SEQUENCE_EXCLUDED_REGION and SEQUENCE_PRIMER_PAIR_OK_REGION_LIST or play with the template. If you're not trying to design PCR primers, I would think that maybe primer3 is not the right tool for the job.