Yang X, Yoshizoe K, Taneda A, Tsuda K. RNA inverse folding using Monte Carlo tree search.
BMC Bioinformatics 2017;
18:468. [PMID:
29110632 PMCID:
PMC5674771 DOI:
10.1186/s12859-017-1882-7]
[Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/26/2017] [Indexed: 11/10/2022] Open
Abstract
Background
Artificially 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.
Result
We 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.
Conclusion
MCTS-RNA is available at https://github.com/tsudalab/MCTS-RNA.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-017-1882-7) contains supplementary material, which is available to authorized users.
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