Hi,

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

Thanks,

N.

R : How To Compute The Melting Temperature Tm

2

Entering edit mode

11.7 years ago

Nicolas Rosewick
11k

Hi,

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

Thanks,

N.

4

Entering edit mode

3.7 years ago

manojmonmax
▴
90

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

2

Entering edit mode

11.7 years ago

JC
13k

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.

1

Entering edit mode

11.7 years ago

KCC
★
4.1k

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.

0

Entering edit mode

11.7 years ago

Malachi Griffith
20k

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.

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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