[Bioperl-l] Bio::SeqFeature::Primer Calculating the Primer TM

[Brad Chapman]

Hey all;

John:
> > At the moment I don't have the code but I guess the easiest way could
> > be to look at the source code of Primer3 and see what the C code looks
> > like (I am assuming it is C) for calculating the Primer TM. 

Jason:
> I believe biopython guys have dealt with this recently -- brad - can you
> point us to working code/documentation for Tm calculation?

Yes, Sebastian Bassi was working on this code for a while. He did
come up with a version, but it turned out to not be the most current
parameters, I believe. I don't think he finished the new version
yet. But, there has been plenty of talk about it -- here's the
relevant mails:

Sebastian's original message:
http://www.biopython.org/pipermail/biopython/2003-November/001701.html

Implementations (for DNA and RNA):
http://www.biopython.org/pipermail/biopython/2003-November/001742.html
http://www.biopython.org/pipermail/biopython/2003-November/001745.html

Mail from Peter Slickers with the information about the most current
accepted parameter sets:
http://www.biopython.org/pipermail/biopython/2003-November/001747.html

Hope this helps you guys -- and reminds Sebastian we'd still
eventually like to see this in Biopython :-).
Brad