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

[Jason Stajich]

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

-jason
On Tue, 17 Feb 2004, john herbert wrote:

> Hello Rob,
> Thanks for the reply. I agree about Primer3 documentation, had me
> puzzled for a while before I sussed it.
>
> 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. Then try to
> mimic it in Perl. If I get time soon, I will have a look. Alternatively
> we could look at the references.
>
> If there are TM Gurus  out there who have a better suggestion, please
> mail us.
>
> Kind regards,
>
> John.
>
> >>> Rob Edwards <redwards at utmem.edu> 17/02/2004 03:40:40 >>>
> I wrote this implementation of the Bio::SeqFeature::Primer module, and
>
> I am guilty as charged. I was confused by the primer3 documentation,
> but hey, at least I was honest in the docs - I said that I couldn't
> figure out what was going on.
>
> I don't know what the formula is that Primer3 used. If you have some
> code for this I can update the module.
>
> Rob
>
>
>
>
> On Feb 12, 2004, at 5:50 AM, john herbert wrote:
>
> > Hello BioPerl.
> > I was thinking of using BioPerl to calculate the Tm of my primers. I
> > looked from the documentation and found the method for getting a
> > primer's Tm. my $tm = $primer->Tm;
> >
> > In the notes of this method, the author is confused by the fact that
> a
> > BioPerl calculated Tm never matches that of Primer3's prediction.
> This
> > is because Primer3 uses a different method to calculate a Primers TM
> > than the method used in the BioPerl.
> >
> >  BioPerl $primer->Tm = Calculated using: Tm = 81.5 +
> 16.6(log10([Na+]))
> > + .41*(%GC) - 600/length
> > (Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11.46 (1989,
> CSHL
> > Press).
> >
> > Primer3 primer TM = Primer3 uses the oligo melting temperature
> formula
> > given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol
> 18,
> > num 12, pp 6409-6412 and Breslauer, Frank, Bloeker and Marky, Proc.
> > Natl. Acad. Sci. USA, vol 83, pp 3746-3750. This method uses
> > thermodynamics to calc TM.
> >
> > Primer3 does use the Sambrook method to predict the TM of the PCR
> > products but not the Primer TM.
> >
> > Would it be possible to update the BioPerl to match how Primer3
> > calculates the Primer TM?
> >
> > Kind regards,
> >
> > John Herbert
> >
> > Cancer Research UK.
> >
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu