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

Published: 01 Jan 2024, Last Modified: 16 May 2025Theor. Comput. Sci. 2024EveryoneRevisionsBibTeXCC BY-SA 4.0
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 5252 to 7373; as for the MBPS, the approximation factor is improved from 8383 to 5252.
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