Then for each of these random sequences from QR set, we built global alignment and for each alignment we determined the values Δ G = G r2) − G r1).
Then we built a global alignment for each random sequence from QT set, and for each alignment, we determined the values Δ G(T) = G t2) − G t1).
From this alignment, we determined all the couples of positions that were statistically never found mutated together, that we called SL and focused on the SL set, which are accessible to the solvent, and not too far apart spatially.
Finally, for each alignment, we determined the probability that a site was polymorphic using the Polybayes program [ 50], with the probability set at greater than 0.99 and a minimum Phred of Q45 [ 51, 52].
By analysis of the spectral alignment we determined 6 highly significant wavenumbers that could be associated with prominent and interpretable second derivative peaks in both groups (labelled as A-F in Figure 2).
To account for biases in the distribution resulting from differences in the frequency of occurrence of each amino acid in the alignments, we determined the statistically expected outcome for repeating this calculation using randomly selected residue pairs but weighting them by the ZRes values of the original coevolving pairs.
In order to quantitatively compare the alignments, we determined their total length.
From these alignments we determined whether each SNP putatively segregating between host races is synonymous or nonsynonymous.
On the basis of the extracted alignments, we determined the fraction of all mouse exon nucleotides that are perfectly conserved in human, and the fraction of human exon nucleotides that are conserved in mouse.
After filtering for orthologs with congruent N-terminal alignments we determined 4,683 cliques and 6,667 gene pairs for the MPSS data, and for YALE-1 and YALE-2 4263 cliques with 4,395 pairs, and 2,185 cliques with 2,379 pairs.
