help for computing relative mCpG density

[chinamrwu]

Hi :
Anybody can help me ?
I am computing the relative DNA methylated Cytosine density of genome, and
confused by the following question:
the DNA sequence is AACGCTT and the methylation level of CGC are 0.6, 0.8,1.0 respectively. Now, is the retio of mCG values to total numbers of CGs
is (0.6+0.8)/2=0.7 or (0.8+1.0)/2=0.9 or (0.6+0.8+1.0)/3=0.8 or [(0.6+0.8)/2+(0.8+1.0)/2]/2=0.8 ? which is correct among the four methods ?

thanks

[C.R.]

In my understanding it is like this: the sequence you provide contains one CpG site which can be sequence from forward and reverse strand. However, if you want to calculate the methylated cytosine density from all cytosines (and you do not restrict yourself to CpG sites) it will be more complex. On the other hand people usually discriminate between CpG, CHG and CHH.