Figure 1

An example of a sequence alignment and a relative entropy calculation. This example shows the calculation of the relative entropies along the neighbouring-nucleotide positions of substitutions (C→T) that occurred at the third-codon positions. In an extracted sequence, the substitution position is labelled as 0, the 5' flank as negative and the 3' flank as positive. Extracted sequences are aligned by these corresponding positions so that the alignment is kept in the same reading frame. The frequencies P(X _i ) of four types of nucleotides for each column of this alignment are then used to calculate the relative entropy at each neighbouring-nucleotide position (see Equation 1). In this example, all nucleotides at site 0 (the substitution site) are T and the relative entropy approximates - log₂ [Q(X _T )]≈ 2 bits at this site.