Parity Rule 2 Plot Analysis

The Parity rule 2 (PR2) plot analysis was used to identify the effects of natural selection and mutation on codon usage bias, which is characterized by the value of AT-bias [A₃/(A₃ + T₃)] as the ordinate and GC-bias [G₃/(G₃ + C₃)] as the abscissa (Sueoka, 1995). A_3, T_3, G₃ and C₃ correspond to the A, T, G, and C content at the third position of four-codon amino acids, respectively. In this plot, the center, where both coordinates are 0.5 (means A = T and G = C), indicates that mutation and selection have an equal effect on codon usage (Sueoka, 1995, 1999).