Fast RNA-RNA interaction prediction considering higher order structure

2014 Fiscal Year Final Research Report

• Project/Area Number: 24700296
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Kyoto University (2014); Nara Institute of Science and Technology (2012-2013)
• Principal Investigator: KATO Yuki 京都大学, iPS細胞研究所, 特定拠点助教 (10511280)
• Project Period (FY): 2012-04-01 – 2015-03-31
• Keywords: RNA間相互作用 / アクセシビリティ / 数理計画法

Outline of Final Research Achievements

In this study, we developed a fast and accurate prediction model for RNA-RNA interactions using integer programming, which can formulate various combinatorial problems appearing in the actual world. Here we incorporated accessibility, probability of being involved in interaction, into the formulation of the integer programming problem, achieving much better predictive performance compared with existing methods that do not consider accessibility. As our proposed method can predict interaction sites in base pair resolution more accurately than the earlier methods can do, this work is expected to greatly contribute to functional analysis of regulatory RNAs.

Free Research Field

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