I want to generate a graph showing the relative evolutionary constraints on single positions of a certain sequence of amino-acids (protein sequence).
I came across this attached figure of E.V. Koonin in his book "The Logic of Chance", what he called "genomescape", is there any method to measure evolutionary constraints per residue in a sequence of amino acids, and generate such a graph?
Thanks
You said you are interested in generating a constraint graph only for a protein sequence (rather than the full gene). The general principles would be similar. First you need to have an alignment that will allow you to measure the evolutionary constraint at each position. For proteins, I recommend generating it using HHblits.
Then you need to calculate a score for each position in the alignment - various scores exist, the most commonly used is probably weighted entropy, implemented here:
https://github.com/gcollet/MstatX
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