Journal
PATTERN RECOGNITION
Volume 42, Issue 4, Pages 531-538Publisher
ELSEVIER SCI LTD
DOI: 10.1016/j.patcog.2008.08.004
Keywords
RNA-RNA interaction; Joint secondary structure; Kissing hairpin; Multiple context-free grammar
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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. (C) 2008 Elsevier Ltd. All rights reserved.
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