New approximation algorithms for RNA secondary structures prediction problems by local search

Abstract

This paper investigates two combinatorial problems from RNA secondary structure prediction with arbitrary pseudoknots. Given a RNA sequence and a set of base pairs, two parallel and adjacent base pairs constitute a stacking. The Maximum Stacking Base Pairs problem (MSBP) aims at finding a maximum number of based pairs, all of which form stackings, while the Maximum Base Pair Stackings problem (MBPS) is to find a maximum number of stackings. Both problems are NP-hard. We present two new approximation algorithms for the two problems by local search methods. For MSBP, the approximation factor is improved from 52 to 73; as for the MBPS, the approximation factor is improved from 83 to 52.