Check For Primer Mixing

Question

[David A.]

Hi,

I have a set of 30 primer pairs that have check individually for specificity using Primer Blast. So each pair should amplify my region of interest with sufficient specificity. But I am wondering if there is any tool that feeding the whole list as FASTA or something similar could check if new primers pairs could be formed and give PCR product from any other combination of my original pairs. As an example, if I have:

Pair1 with Primer1 - Primer2, for amplicon1

and

Pair 2 with Primer3 - Primer4, for amplicon2

how can I check in silico whether unwanted pairs that can amplify anything in the human genome of the example types:

Primer1 - Primer3 amplifying ampliconY

Primer3 - Primer2 amplifying ampliconZ

Thanks for any input.

Best,

Dave

Answer 1

[seidel]

You could use epcr (from NCBI) on the command line to evaluate every combination of pairs. I don't know of anything that would do the combinations for you, but you could easily build them yourself.

[David A.]

Thanks Seidel, I have tried epcr and it seems to work fine. I have also found ipcress which seems to be similar to epcr.