Prediction of RNA secondary structure based on stem region replacement using the RSRNA algorithm

Abstract

RNA functions, including the regulation of various cellular activities, seem to be closely related to its structure. However, accurately predicting RNA secondary structures can be difficult. Structural prediction can be achieved by selecting stem areas that are suitable and compatible from stem pools. Here, we propose a method for predicting the secondary structure of non-coding RNA based on stem region substitution, which we named RSRNA. This method is compatible with nested RNA secondary structures, while reducing any randomness. Our algorithm had higher performance and prediction accuracy than other algorithms, which deems it more effective for future RNA structure studies.

Keywords:

• RNA secondary structure
• rsRNA
• stem pool
• combinatorial optimization algorithm

Acknowledgment

We would like to thank Editage (www.editage.cn) for their English language editing.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This work was supported by the Natural Science Foundation of Anhui Province (1908085QF286), the National Natural Science Foundation of China (31500594), the key projects of Natural Science Foundation of Anhui Provincial Department of Education (KJ2020A0031, KJ2020A0037, KJ2019A0603), and the 2017 Anhui Provincial Key Laboratory of medical physics and technology open fund (LMPT201706).