Tools For Calculating Accurate Primer-Target Tm'S (With Mismatches)?

Question

[edwardbeaty]

Hi! I just found this site from reddit, and thought I'd ask this question here as well. I have a large number of DNA primer-target pairs for which I need to calculate the melting temperature. The trick is that some of the pairs will have mismatches, and I want the numbers to as closely reflect physical reality as possible. In addition, I want to run the program locally. I've used the DNA Software OMP package before, but due to licensing considerations am eager to find a different package that still gives accurate Tm numbers. Does anyone have any recommendations?

Answer 1

[Khader Shameer]

You can use PerlPrimer to calculate primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. Manuscript describing PerlPrimer here.

You can also use EMBOSS (See dan, primersearch and ePrimer3).