Question: Designing Primers For Multiplex Pcr
gravatar for rob
7.0 years ago by
rob30 wrote:

I have a 2kb region of DNA, and I need to design five non-overlapping primer pairs to any location within this same stretch of DNA. I need to use all of these primers together in the same PCR reaction, so they must be multiplex compatible (e.g. not have any complementarity to each other). Does anyone know of any software that can do this automatically? Or of rules for filtering a whole load of Primer3 output primers to select the top five that might work in a multiplex pcr?

Thanks for the help!

primer pcr • 7.8k views
ADD COMMENTlink modified 2.1 years ago by Biostar ♦♦ 20 • written 7.0 years ago by rob30
gravatar for Dan D
7.0 years ago by
Dan D7.1k
Dan D7.1k wrote:

I think PCRTiler can do what you need.

ADD COMMENTlink written 7.0 years ago by Dan D7.1k

Yes, that looks like it will do exactly what I want - thanks!

ADD REPLYlink written 6.9 years ago by rob30
gravatar for Felix Francis
3.5 years ago by
Felix Francis510
United States/University of Delaware
Felix Francis510 wrote:

ThermoAlign is a primer design tool for tiled amplicon sequencing (includes multiplexing) using highly specific primers:


ADD COMMENTlink written 3.5 years ago by Felix Francis510
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