Improving the Alignment Quality of Consistency Based Aligners with an Evaluation Function Using Synonymous Protein Words
Figure 3
The dot matrix generated by SymAlign for proteins BB11002.1bb9 and BB11002.1ov3_A in RV11.
A grayscaled dot represents the number of shared synonyms corresponding to a residue pair. We turn a grayscaled dot into a red-scaled one if the corresponding residue pair is annotated as an equivalent pair in the reference alignment. As one can see, the left side of the matrix shows an alternative alignment with a pattern very similar to the reference alignment.