Using the concept of pseudo amino acid composition to predict resistance gene against Xanthomonas oryzae pv. oryzae in rice: An approach from chaos games representation

To evaluate the possibility of an unknown protein to be a resistant gene against Xanthomonas oryzae pv. oryzae, a different mode of pseudo amino acid composition (PseAAC) is proposed to formulate the protein samples by integrating the amino acid composition, as well as the Chaos games representation (CGR) method. Some numerical comparisons of triangle, quadrangle and 12-vertex polygon CGR are carried to evaluate the efficiency of using these fractal figures in classifiers. The numerical results show that among the three polygon methods, triangle method owns a good fractal visualization and performs the best in the classifier construction. By using triangle + 12-vertex polygon CGR as the mathematical feature, the classifier achieves 98.13% in Jackknife test and MCC achieves 0.8462.

► We use improved chaos games presentation method to predict Xoo-resistant gene. ► Triangular and quartic figures are incorporated into CGRs. ► The classifier achieves 98.13% in Jackknife test and MCC achieves 0.8462. ► Constructed classifier is used to predict unknown genes in KOME.