The OMES score at position [i,j] has been computed with the following formula :
$${OMES(i,j)} = \frac{1}{N(i,j)} \sum_{x,y}^{ }(N_{x,y}^{obs}(i,j)-N_{x,y}^{ex}(i,j))^2$$
with : \(N_{x,y}^{ex}(i,j) = p_{x}(i)p_{y}(j)N\)
where :
\(N_{x,y}^{obs}(i,j)\)is number of times that each (x,y) pair is observed at positions i and j
\(N_{x,y}^{ex}(i,j)\)is number of times that each (x,y) pair would be expected, based on the frequency of residues x and y at positions i and j
\(N(i,j)\)is the number of sequences in the alignment with non-gapped residues at positions i and j
\(p_{x}(i)\)is the frequency of amino acid x at position i
\(p_{y}(j)\)is the frequency of amino acid y at position j