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Updated: Jun 18, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Dynamic programming algorithms for RNA structure prediction with binding sites
Unyanee Poolsap1, Yuki Kato, Tatsuya Akutsu
1Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan. unyanee@kuicr.kyoto-u.ac.jp
Abstract:
Noncoding antisense RNAs have recently occupied considerable attention and several computational studies have been made on RNA-RNA interaction prediction. In this paper, we present novel dynamic programming algorithms for predicting the minimum energy secondary structure when binding sites of one of the two interacting RNAs are known. Experimental results on several known RNA-RNA interaction data show that our proposed method achieves good performance in accuracy and time.
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