R : How To Compute The Melting Temperature Tm

Question

[Nicolas Rosewick]

Hi,

Is there a R package to compute the Tm of a dna sequence ?

Thanks,

N.

Answer 1

[manojmonmax]

Hello,

There is a simple formula to calculate the melting temperature of a primer

• If you have a sequence that is less than 14 nucleotides, then you can use the formula :

Melting temperature(°C) = (nA+nT) 2 + (nG+nC) 4

• If you have a sequence that is greater than 14 nucleotides, then you can use the formula :

Melting temperature(°C) = 64.9 + 41 * (nG+nC-16.4)/(nA+nT+nG+nC)

where,

• nA : Number of adenine bases in the sequence
• nT : Number of thymine bases in the sequence
• nC : Number of cytosine bases in the sequence
• nG : Number of guanine bases in the sequence

Answer 2

[JC]

I'm not aware of a package with the formula, but you can use the the Wallace rule for an approximation in short sequences (primers):

Tm = 2°C(A+T) + 4°C(G+C)

Or the Howley formula for longer sequences:

Tm = 81.5 + 0.4m1(%GC) – 500/L + 16.6 log[M]

where L refers to the length of the oligonucleotide, and [M] is the concentration of monovalent cations.

Answer 3

[KCC]

If you know python (or can manage to read it reasonably well), then you can translate this function into R: http://biopython.org/DIST/docs/api/Bio.SeqUtils.MeltingTemp-pysrc.html#Tm_staluc

It's not a very lengthy function, and would probably not take very long.

[liuwei]

Hi, How to get the latest Biopython with the current version of Tm_staluc? As my matchine is a old version,it cannot use of function of Tm_NN. Thanks

Answer 4

[Malachi Griffith]

Once upon a time I wrote a simple Perl script that will do this. Similar to the Python script suggested by 'George' this script uses a nearest neighbor approach. The nearest neighbor and thermodynamic calculations are done essentially as described by Breslauer et al., (1986) Proc. Nat. Acad. Sci. 83:3746-50 but using the thermodynamic data values published by Sugimoto et al., (1996) Nucl. Acids Res. 24:4501-4505. It assumes that the sequences are not symmetric and contain at least one G or C. The minimum length for the query sequence is 8.

Converting it to R should not be too painful hopefully.

getNearestNeighborTm.pl