Predicting RNA Secondary Structure Using a Improved BPSO Based on Stem Combination

Abstract

In this paper, we present an improved BPSO to predict RNA secondary structure to improve the performance with two new strategies. First one is to reduce the searching space of PSO through super stem set construction. Second is to modify the general BPSO updating process to settle stem permutation and combination problems. The experimental results show that the new method is effective for RNA structure prediction in terms of sensitivity and specificity by different sequence datasets including simple pseudoknot.