I am a PhD student new to the field of genetics and bioinformatics.
I am trying to find a more reliable way to count the number of CG sites in the 5' flanking regions of my genes and number them with reference to the ATG start codon.
I have accomplished this primitively by cutting and paste DNA sequences downloaded from the NCBI website and finding CG on MS Word, and counting them one by one.
While this method is fine, I would prefer to check my work against a software with some algorithms in place. However, most of the sites I have found only show CpG islands instead of numbering each site on a sequence map.
My question is if there is a more efficient way to list all the CG sites in a given sequence.
If anyone has any suggestions, I would greatly appreciate it!