Approximation Algorithms for Predicting RNA Secondary Structures with Arbitrary Pseudoknots

We study three closely related problems motivated by the prediction of RNA secondary structures with arbitrary pseudoknots: the problem 2-Interval Pattern proposed by Vialette [36], the problem Maximum Base Pair Stackings proposed by Leong et al. [16], and the problem Maximum Stacking Base Pairs proposed by Lyngso [21]. For the 2-Interval Pattern, we present polynomial-time approximation algorithms for the problem over the preceding-and-crossing model and on input with the unitary restriction. For Maximum Base Pair Stackings and Maximum Stacking Base Pairs, we present polynomial-time approximation algorithms for the two problems on explicit input of candidate base pairs. We also propose a new problem called Length-Weighted Balanced 2-Interval Pattern, which is natural in the context of RNA secondary structure prediction.