Reverse Engineering Approach in Molecular Evolution: Simulation and Case Study with Enzyme Proteins

We developed a method of reverse engineering to compare the behaviour the enzyme proteins with the existing standard concepts. Our work is based on the strong assumption from the evolutionary theory, about the rates of nucleotide substitutions; we use this in the reverse engineering approach to verify how far it can be justified. We applied here the simple models of nucleotide substitutions Nei and Gojobori in a more generalized form and used comparative genomic study with human, mouse and rat individually with related enzyme proteins. We then used Jukes and Cantor’s model to find out the corrected substitution rates. This paper describes the findings and the methodology in details.