Figure 4
The distribution of synonymous words shared by 1aab and 1j46_A. The x- and y- axes represent the sequence of 1j46_A and 1aab respectively. A grayscale pixel represents the number of shared synonymous words corresponding to a residue pair (x i , y j ), where xi and y j denote a residue pair comprised of the i-th residue of 1j46_A and the j-th residue of 1aab respectively. Box B is a zoom-in of Box A. The red lines indicate the alignment based on the number of shared synonymous words, and the alignment is very close to that reported in Balibase for the two proteins. Notably, it can be observed that the path of the darker pixels is nearly perfectly matched the suggested alignment.