RNA inverse folding using Monte Carlo tree search

BMC Bioinformatics

Methodology Article

Xiufeng Yang¹  Koji Tsuda²  Akito Taneda³  Kazuki Yoshizoe⁴ 

[1] Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, 277-8561, Kashiwa, Japan;Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, 277-8561, Kashiwa, Japan;Center for Materials Research by Information Integration, National Institute for Materials Science, 1-2-1 Sengen, 305-0047, Tsukuba, Japan;RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihombashi Chuo-ku, 103-0027, Tokyo, Japan;Graduate School of Science and Technology, Hirosaki University, 3 Bunkyo-cho, 036-8561, Hirosaki, Japan;RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihombashi Chuo-ku, 103-0027, Tokyo, Japan;

关键词: Monte Carlo tree search;    RNA inverse folding;    Local update;    Pseudoknotted structure;   

DOI  :  10.1186/s12859-017-1882-7

 received in 2017-02-08, accepted in 2017-10-26,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundArtificially synthesized RNA molecules provide important ways for creating a variety of novel functional molecules. State-of-the-art RNA inverse folding algorithms can design simple and short RNA sequences of specific GC content, that fold into the target RNA structure. However, their performance is not satisfactory in complicated cases.ResultWe present a new inverse folding algorithm called MCTS-RNA, which uses Monte Carlo tree search (MCTS), a technique that has shown exceptional performance in Computer Go recently, to represent and discover the essential part of the sequence space. To obtain high accuracy, initial sequences generated by MCTS are further improved by a series of local updates. Our algorithm has an ability to control the GC content precisely and can deal with pseudoknot structures. Using common benchmark datasets for evaluation, MCTS-RNA showed a lot of promise as a standard method of RNA inverse folding.ConclusionMCTS-RNA is available at https://github.com/tsudalab/MCTS-RNA.

【 授权许可】

CC BY   
© The Author(s) 2017