A generalization of CGR representation for analyzing and comparing protein sequences

Abstract

Based on three kinds of physiochemical properties of amino acids, twenty amino acids are divided into eight groups, and replaced at eight vertices of a cube. Then, we present a new way of generalized Chaos Game Representation (CGR) method to outline a dynamic 3D graphical representation called HPL curve. Furthermore, the mathematical descriptor is suggested to characterize the similarities/dissimilarities of two HPL curves. The usefulness of this approach can be illustrated by performing the comparison of sequences of ND6 proteins of eight species, as well as sequences of sixteen ND5 proteins. By the correlation analysis, ClustalW results were compared with our results and some other graphical representation results to demonstrate the effectiveness of our approach.