Maximum stacking base pairs is a fundamental combinatorial problem from RNA secondary structure prediction under the energy model. The basic maximum stacking base pairs problem can be described as: given an RNA sequence, find a maximum number of base pairs such that each chosen base pair has at least one parallel and adjacent partner (i.e., they form a stacking). This problem is NP-hard, no matter whether the candidate base pairs follow the biology principle or are given explicitly as input. This paper investigates a restricted version of this problem where the base pairs are given as input and each base is associated with at most k (a constant) base pairs. We show that this restricted version is still APX-hard, even if the base pairs are weighted. Moreover, by a nonlinear LP-rounding method, we present an approximation algorithm with a factor Applying our algorithms on the simulated data, the actual approximation factor is in fact much better than this theoretical bound.
CITATION STYLE
Liu, L., Jiang, H., Liu, P., Zhu, B., & Zhu, D. (2019). Maximum Stacking Base Pairs: Hardness and Approximation by Nonlinear LP-Rounding. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 11490 LNBI, pp. 244–256). Springer Verlag. https://doi.org/10.1007/978-3-030-20242-2_21
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