A grammatical approach to RNA-RNA interaction prediction

Authors:
Yuki Kato;Tatsuya Akutsu;Hiroyuki Seki
Affiliations:
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan;Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan;Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
Venue:
Pattern Recognition
Year:
2009

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Abstract

Much attention has been paid to RNA-RNA interaction involved in posttranscriptional regulation of gene expression. Although there have been a few studies on secondary structure prediction of interacting RNAs using dynamic programming (DP) algorithms, no grammar-based approach has been proposed. This paper provides a new modeling for RNA-RNA interaction based on multiple context-free grammar (MCFG). We present a polynomial time parsing (prediction) algorithm of the stochastic version of MCFG. Experimental results show that our approach is comparable to an existing work based on DP. The MCFG-based approach is more flexible than other DP-based methods.