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

被引：0

作者：

Zhou, Aizhong ^{[1
,2
]}

Feng, Haodi ^{[1
]}

Guo, Jiong ^{[1
]}

Jiang, Haitao ^{[1
]}

Liu, Nan ^{[3
]}

Zhu, Binhai ^{[4
]}

Zhu, Daming ^{[1
]}

机构：

[1] Shandong Univ, Sch Comp Sci & Technol, Qingdao, Shandong, Peoples R China

[2] Ocean Univ China, Sch Comp Sci & Technol, Qingdao, Shandong, Peoples R China

[3] Shandong Jianzhu Univ, Sch Comp Sci & Technol, Jinan, Shandong, Peoples R China

[4] Montana State Univ, Gianforte Sch Comp, Bozeman, MT 59717 USA

来源：

THEORETICAL COMPUTER SCIENCE | 2024年 / 988卷

基金：

中国国家自然科学基金;

关键词：

RNA secondary structure prediction; Approximation algorithm; Local search;

D O I：

10.1016/j.tcs.2023.114354

中图分类号：

TP301 [理论、方法];

学科分类号：

081202 ;

摘要：

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 38 to 52.

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页数：11

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