A grammatical approach to RNA-RNA interaction prediction
A grammatical approach to RNA-RNA interaction prediction
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DOI：
10.1016/j.patcog.2008.08.004
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发表时间：
2009-04-01
影响因子：
8
通讯作者：
Seki, Hiroyuki
中科院分区：
文献类型：
--
作者：
Kato, Yuki;Akutsu, Tatsuya;Seki, Hiroyuki
RNA-RNA相互作用参与基因表达的转录后调控，已经引起了人们的广泛关注。虽然已经有一些研究使用动态规划(DP)算法来预测相互作用的RNA的二级结构，但还没有人提出基于语法的方法。提出了一种基于多上下文无关文法(MCFG)的RNA-RNA相互作用模型。提出了MCFG的随机版本的多项式时间解析(预测)算法。实验结果表明，我们的方法可以与现有的基于DP的方法相媲美。基于MCFG的方法比其他基于DP的方法更灵活。(C)2008爱思唯尔有限公司。保留所有权利。
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.