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?
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written
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edwardbeaty •
1 answer
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).
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