[BioPython] Re: [Bioperl-l] Bio::SeqFeature::Primer Calculating the Primer TM (fwd)

Jason Stajich jason at cgt.duhs.duke.edu
Tue Feb 17 16:03:27 EST 2004

Sebastian's comments cross-posted.

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

---------- Forwarded message ----------
Date: Tue, 17 Feb 2004 18:10:43 -0300
From: Sebastian Bassi <sbassi at asalup.org>
To: Brad Chapman <chapmanb at uga.edu>
Cc: biopython at biopython.org
Subject: Re: [BioPython] Re: [Bioperl-l] Bio::SeqFeature::Primer
    Calculating the Primer TM

Brad Chapman <chapmanb at uga.edu> Escribio
> Hope this helps you guys -- and reminds Sebastian we'd still
> eventually like to see this in Biopython :-).

I now. I am a little busy right now (have you hear of DNALinux?, I'm working
on it and some academic projects also!).
But I want to code the function. What is holding me now (appart from lack of
time) is that I didn't find a working source code of Santalucia's formulae. I
tried to follow the paper but I couldn't. An implamentation, even in C or
pseudocode, would help me. Another thing that will be usful, would be some
pre-made Tm calculation using Santalucia parameters. This will be useful to
test my code.
What I did was very close since it worked as EMBOSS DAN, but Santalucia is
the way to go.

Sebastian Bassi. PGP Key available.

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