[Bioperl-l] Tm calculation using thermodynamic concept for Degenerate Primers?

Giles Weaver giles.weaver at googlemail.com
Wed Apr 14 17:08:43 EDT 2010

Hi Bhakti,

My old code for calculating degenerate PCR primer Tm has been lurking
unloved on my computer for a while, so I've uploaded some snippets to
the BioPerl wiki scrapbook at

The code uses BioPerl together with Primer 3. I don't have a pure perl
implementation. I can't remember what Tm calculation methods are
available through Primer 3, but I believe there are several methods in
the documentation. I haven't seen a method for calculating the Tm of
primers with Inosine, but that may not matter to you.

The constituents of degenerate primers can have a wide range of
melting temperatures, so finding forward and reverse primers that
operate within an acceptable range could be tricky. As for what
constitutes an acceptable temperature range, I suggest you consult
your nearest friendly PCR technician. If you get any sensible answers
please report back.

I hope this helps, please let me know how you get on.


P.S. Apologies for the re-post, HTML email bad...

On 14/04/10 18:20, Bhakti Dwivedi wrote:

Does anyone know how to compute the melting temperature for Degenerate
Primers following the thermodynamic nearest neighbor model?  or how it
works? what I found so far is Tm calculations for primers with A,C,G, or T
only, but haven't came across anything that can help me explain the way it
works for degenerate primers, so I can implement that in my perl code.

any help please? Thanks!

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