In order to compute dn/ds (the ratio of synonymous to non-synonymous substitutions in a mutated sequence), I need to first calculate the number of synonymous and non-synonymous sites in a coding sequence. I've been doing this rather tediously the "brute force" way, i.e. obtaining exons for each coding sequence, concatenating, and then looping through reading frames with a genetic code dictionary to compute the fractional synonymous/non-synonymous point mutations possible for each site.
Surely there is some simple tool (perhaps on Biomart / using bioconductor) that allows one to enter the Hugo symbol or some other CDS idea that will just provide these counts, but I haven't been able to find it.
If such a resource exists, please direct me to it.
Thanks. I posted the same question nearly a year ago and forgot both about it and the response.