RNA-RNA Interaction Prediction Using Integer Programming with Threshold Cut

• Item type: SIG Technical Reports(1)
• 公開日: 2010-06-11
• タイトル: RNA-RNA Interaction Prediction Using Integer Programming with Threshold Cut
• タイトル / 言語: en
• タイトル: RNA-RNA Interaction Prediction Using Integer Programming with Threshold Cut
• 言語: eng
• 資源タイプ / 資源タイプ識別子: http://purl.org/coar/resource_type/c_18gh
• 資源タイプ: technical report
• 著者所属: Bioinformatics Center, Institute for Chemical Research, Kyoto University
• 著者所属: Graduate School of Frontier Sciences, University of Tokyo
• 著者所属: Mizuho Information & Research Institute, Inc／Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
• 著者所属: Department of Mathematical Sciences, Faculty of Science and Engineering, Doshisha University
• 著者所属: Graduate School of Frontier Sciences, University of Tokyo／Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
• 著者所属: Bioinformatics Center, Institute for Chemical Research, Kyoto University
• 著者所属(英): en
• 著者所属(英): Bioinformatics Center, Institute for Chemical Research, Kyoto University
• 著者所属(英): en
• 著者所属(英): Graduate School of Frontier Sciences, University of Tokyo
• 著者所属(英): en
• 著者所属(英): Mizuho Information & Research Institute, Inc / Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
• 著者所属(英): en
• 著者所属(英): Department of Mathematical Sciences, Faculty of Science and Engineering, Doshisha University
• 著者所属(英): en
• 著者所属(英): Graduate School of Frontier Sciences, University of Tokyo / Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
• 著者所属(英): en
• 著者所属(英): Bioinformatics Center, Institute for Chemical Research, Kyoto University
• 著者名: Yuki, Kato; Kengo, Sato; Michiaki, Hamada; Yoshihide, Watanabe; Kiyoshi, Asai; Tatsuya, Akutsu
• 著者名(英): Yuki, Kato; Kengo, Sato; Michiaki, Hamada; Yoshihide, Watanabe; Kiyoshi, Asai; Tatsuya, Akutsu
• 論文抄録 / 内容記述タイプ: Other
• 論文抄録 / 内容記述: 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.
• 論文抄録(英) / 内容記述タイプ: Other
• 論文抄録(英) / 内容記述: 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.
• 書誌レコードID / 収録物識別子タイプ: NCID
• 書誌レコードID / 収録物識別子: AA12055912
• 書誌情報: 研究報告バイオ情報学（BIO）; 巻 2010-BIO-21, 号 32, p. 1-8, 発行日 2010-06-11
• Notice: SIG Technical Reports are nonrefereed and hence may later appear in any journals, conferences, symposia, etc.
• 出版者 / 言語: ja
• 出版者: 情報処理学会