Effective Number Of Codons (Enc Vs. Gc3 Plot)

Question

[tigeradab]

How to plot the ENC vs GC3 plot showing the curve of expected ENC value? I guess the formula(approximate relationship) given in ENC paper by Wright,1990 has an error. Looking at the formula we can see that always the 29/(s2+(1-s2)) comes to be 29 as s2 cancel out in the denominator. Is there any correction for this? Is there any software that generates ENC vs. GC3 plot?

Answer 1

[rahulravi777]

The formula to be used for calculation is 2+S+ (29/(s2+ (1-s)2)). By this formula, you may get expected ENC values for 0, 0.1, 0.2 ...1 (GC compositions).

[Nitha]

Hi,

I am too facing same problem to plot ENc vs GC3. How to put the curve in the ENc vs GC3 scatter plot.

plz guide me to plot the graph.

Thanks

Answer 2

[Firingam]

I recommend to use the improved version of Sun (Sun et al., 2012) to get a more sophisticated statistic about codon usage. Anyway the question would be clearer if you could specify the programming language you want to use.