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Table 1 presents Pearson's and Spearman's correlation coefficients between the rate and the breadth of evolution, calculated from these data.
Then, a site with a large number of permitted amino acids should display both a high rate and a wide breadth of evolution.
Indeed, on a sample of only 11 or 13 genomes, the "real" values of rate and breadth of evolution are determined, for a particular site, only with substantial sampling errors, which reduces their correlation.
A measure of amino acid diversity which is equivalent to B be has been proposed in [ 6]. Figure 2 shows the relationship between the rate and the breadth of evolution at individual amino acid sites.
The second is the "breadth" of evolution, i. e., the diversity of acceptable amino acids, which can be defined as the probability that two independent replacements of a particular amino acid at a site lead to the same amino acid.
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There is a weak positive correlation between rates and breadths of evolution, both across individual amino acid sites and across proteins.
Given the complexity of HPC, what is presented here is a first attempt to make sense of the breadth of the evolution of HPC in Canada.
A priori, one could expect the rate and the breadth of protein evolution to be positively correlated across sites.
Our data demonstrate a weak positive correlation between the rate and the breadth of protein evolution across both individual sites and whole proteins (Table 1).
Reviewer's report Title: Rate and breadth of protein evolution are only weakly correlated Version: 2 Date: 1 November 2011 Reviewer number: 3 Report form: Review of the paper Rate and breadth of protein evolution are only weakly correlated" by SA Naumenko and AS Kondrashov.
Reviewer's report Title: Rate and breadth of protein evolution are only weakly correlated Version: 2 Date: 5 October 2011 Reviewer number: 2 Report form: The authors demonstrate that the frequency of amino acid substitutions (rate of protein sequence evolution) and the repertoire of replacements in the substituted sites (breadth of protein sequence evolution) are correlated only weakly.
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