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The conformational and physico-chemical features (properties mean values) of the site

For a nucleotide sequence S={s1...si...sL}, of the length L, containing dinucleotide sisi+1 at the i-th position the mean value Xk of the k-th conformational or physico-chemical property averaged over the region [a; b] (1 a b L) of the sequence S is calculated as follows:

Applying equation (1) to the site sequence set {S} at fixed k, a, and b yields the distribution Xk,a,b{S} for the site sequences. Similarly, the distribution, Xk,a,b{R} is generated for random sequences {R} with the same nucleotide frequencies as in the real sequences. The difference between these distributions Xk,a,b{S} and Xk,a,b{R} is tested for significance by calculating of the utility value U(Xk,a,b), which is the integral characteristic of the discriminating ability of Xk,a,b.