Question: Using Rate4Site To Calculate Mutation Rate Per Gene?
1
gravatar for anin.gregory
6.2 years ago by
anin.gregory80
United States
anin.gregory80 wrote:

I would like to calculate the mutation rate per gene based on an MSA. In this past post (C: Mutation rates for a specific gene?) someone suggested using Rate4Site to calculate mutation rate per gene. However the program is specifically designed to calculate the conservation score for each amino acid, with a lower value indicating higher conservation.

I read the associated papers Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues and Comparison of Site-Specific Rate-Inference Methods for Protein Sequences: Empirical Bayesian Methods Are Superior, and I don't understand how you can get from the conservation score to a mutation rate. Maybe I am missing something in the papers. Has anyone tried using Rate4Site to calculate mutation rate per amino acid / per gene??

gene mutation msa • 2.9k views
ADD COMMENTlink modified 6.2 years ago by Asaf5.6k • written 6.2 years ago by anin.gregory80
0
gravatar for Asaf
6.2 years ago by
Asaf5.6k
Israel
Asaf5.6k wrote:

The rate of each position (the r parameter which is the only parameter estimated) appears in the output sent to stdout or to a file using the option -y filename. The conservation scores are just z-scores of these rates, normalized for each gene.

ADD COMMENTlink written 6.2 years ago by Asaf5.6k

I'm sorry. I still don't understand how this is the mutation rate. It is saying that the rate is 0.9999. This does not make sense, since mutation rates are usually in 10^-8 orders of magnitude for my system. Am I doing something wrong? I an MSA and use the default NJ tree option. Thanks in advance.

ADD REPLYlink written 6.1 years ago by anin.gregory80
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