A grammatical approach to RNA–RNA interaction prediction

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...

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Bibliographic Details
Published inPattern recognition Vol. 42; no. 4; pp. 531 - 538
Main Authors Kato, Yuki, Akutsu, Tatsuya, Seki, Hiroyuki
Format Journal Article
LanguageEnglish
Published Elsevier Ltd 01.04.2009
Subjects
Joint secondary structure
Kissing hairpin
Multiple context-free grammar
RNA–RNA interaction
87.15.Cc
Kissing hairpin
Joint secondary structure
Multiple context-free grammar
87.14.Gg
RNA–RNA interaction
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Summary: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.
ISSN:0031-3203
1873-5142
DOI:10.1016/j.patcog.2008.08.004