Question: R : How To Compute The Melting Temperature Tm
2
gravatar for Nicolas Rosewick
8.0 years ago by
Belgium, Brussels
Nicolas Rosewick9.2k wrote:

Hi,

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

Thanks,

N.

R • 5.5k views
ADD COMMENTlink modified 15 days ago by manojmonmax90 • written 8.0 years ago by Nicolas Rosewick9.2k
4
gravatar for manojmonmax
15 days ago by
manojmonmax90
manojmonmax90 wrote:

Hello,

There is a simple formula to calculate the melting temperature of the given Nucleotide Sequence :
  • 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

This formula works pretty well in scripting languages like Perl.

ADD COMMENTlink modified 15 days ago • written 15 days ago by manojmonmax90
2
gravatar for JC
8.0 years ago by
JC12k
Mexico
JC12k wrote:

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.

ADD COMMENTlink written 8.0 years ago by JC12k
1
gravatar for KCC
8.0 years ago by
KCC4.0k
Cambridge, MA
KCC4.0k wrote:

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.

ADD COMMENTlink written 8.0 years ago by KCC4.0k

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

ADD REPLYlink written 3.8 years ago by liuwei0
0
gravatar for Malachi Griffith
8.0 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

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

ADD COMMENTlink written 8.0 years ago by Malachi Griffith18k
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