A new graphical representation of similarity/dissimilarity studies of protein sequences

Abstract

Based on chaos game representation, a two-dimensional-graphical representation of protein sequences is described in which 20 amino acids are rearranged in a cyclic order using a PAM250 substitution matrix. A numerical characterisation has been developed as a descriptor to compare protein sequences. Finally, an example is given in which the dehydrogenase subunit 5 (ND5) protein sequences of nine species are compared.

Keywords:

• protein sequence
• PAM250 matrix
• cyclic order
• amino acids

Acknowledgements

The author thanks the referees for many valuable comments that have improved this manuscript. This work was supported by the Zhejiang Provincial Natural Science Foundation of China (No. Y6090261).