RNA-RNA Interaction Prediction Using Integer Programming with Threshold Cut
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概要
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Much attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of noncoding small RNAs that regulate gene expression post-transcriptionally. A number of computational studies have so far been devoted to predicting joint secondary structures or binding sites under a specific class of interactions. In this technical report, we propose RactIP, a fast and accurate prediction method for RNA-RNA interaction of general type based on integer programming. RactIP can integrate approximate information on an ensemble of equilibrium joint structures into the objective function using posterior internal and external base paring probabilities. Experimental results show that prediction accuracy of RactIP is at least comparable to that of several state-of-the-art methods for RNA-RNA interaction prediction. Moreover, we demonstrate that RactIP can run incomparably faster than competitive methods for predicting joint secondary structures.
- 2010-06-11
著者
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Tatsuya Akutsu
Bioinformatics Center, Institute for Chemical Research, Kyoto University
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Yuki Kato
Bioinformatics Center, Institute for Chemical Research, Kyoto University
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Kengo Sato
Graduate School of Frontier Sciences, University of Tokyo
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Michiaki Hamada
Mizuho Information & Research Institute, Inc|Computational Biology Research Center (CBRC), National
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Yoshihide Watanabe
Department of Mathematical Sciences, Faculty of Science and Engineering, Doshisha University
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Kiyoshi Asai
Graduate School of Frontier Sciences, University of Tokyo|Computational Biology Research Center (CBR
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Kengo Sato
Graduate School Of Frontier Sciences University Of Tokyo
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Kiyoshi Asai
Graduate School Of Frontier Sciences University Of Tokyo|computational Biology Research Center (cbrc
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Michiaki Hamada
Mizuho Information & Research Institute Inc|computational Biology Research Center (cbrc) Nationa
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Tatsuya Akutsu
Bioinformatics Center Institute For Chemical Research Kyoto University
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Tatsuya Akutsu
Bioinformatics Center Institute For Chemical Research Kyoto Univerty
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Yoshihide Watanabe
Department Of Mathematical Sciences Faculty Of Science And Engineering Doshisha University
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Yuki Kato
Bioinformatics Center Institute For Chemical Research Kyoto University
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Kato Yuki
Bioinformatics Center Institute For Chemical Research Kyoto University
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