2011 Fiscal Year Final Research Report
RNA-RNA interaction prediction using hybrid optimization
| Project/Area Number |
22700313
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| Research Category |
Grant-in-Aid for Young Scientists (B)
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| Allocation Type | Single-year Grants |
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| Research Field |
Bioinformatics/Life informatics
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| Research Institution | Nara Institute of Science and Technology |
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Principal Investigator |
KATO Yuki 奈良先端科学技術大学院大学, 情報科学研究科, 助教 (10511280)
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| Project Period (FY) |
2010 – 2011
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| Keywords | RNA間相互作用 / RNA2次構造 / キッシングヘアピン / シュードノット / 整数計画法 |
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| Research Abstract |
In this work, we developed a novel method for RNA joint secondary structure prediction that aims at RNA. RNA interaction prediction by integrating the maximizing expected accuracy principle with integer programming. Furthermore, based on the idea of the proposed method, we presented an algorithm for predicting RNA secondary structures with pseudoknots, a class of complex substructures, when a single RNA sequence is given. Experimental results on real data sets indicate that both methods are at least comparable in prediction accuracy to existing methods, and even more importantly, are overwhelmingly faster than the early predictors. A web server that implements the proposed methods is free and open to all users.
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