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

john herbert john.herbert at clinical-pharmacology.oxford.ac.uk
Thu Feb 12 06:50:45 EST 2004

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
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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