Question: Is there a tool for counting the number of non-synonymous sites in a CDS
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gravatar for Max
3.4 years ago by
Max130
Max130 wrote:

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.

ensembl dnds biomart cds • 1.3k views
ADD COMMENTlink modified 3.4 years ago by natasha.sernova3.6k • written 3.4 years ago by Max130
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gravatar for natasha.sernova
3.4 years ago by
natasha.sernova3.6k
natasha.sernova3.6k wrote:

According to Emily, there is no tool like that in Biomart.

Ensembl biomart attribute for number of synonymous vs. non-synonymou sites

You can use PAML to calculate the ratio.

Phylogenetic Analysis By Maximum Likelihood (Paml)

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by natasha.sernova3.6k

Thanks. I posted the same question nearly a year ago and forgot both about it and the response.

ADD REPLYlink written 3.4 years ago by Max130
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