Algorithm and Scheme in RNA Structure Prediction Including Pseudoknots

Abstract

It is an NP-hard problem for prediction of RNA folding structure incuding pseudoknots, we investigate the RNA pseudoknotted structure based on characteristics of the RNA folding structure, and the Basin Hopping Graph as a novel model of RNA folding landscape structures. Our paper design an 1+ε (ε>0) polynomial time approximation scheme in searching maximum number of stackings, we give the proof of the approximation scheme in RNA pseudoknotted structure. we have also presented the computing algorithm of barrier tree based on the BHG.