Ultra-fast RNA structural alignments with pseudoknots

2016 Fiscal Year Final Research Report

• Project/Area Number: 25330348
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Life / Health / Medical informatics
• Research Institution: Keio University
• Principal Investigator: Sato Kengo 慶應義塾大学, 理工学部(矢上), 講師 (20365472)
• Project Period (FY): 2013-04-01 – 2017-03-31
• Keywords: RNA二次構造 / 構造アラインメント / 期待精度最大化 / 双対分解 / 整数計画法

Outline of Final Research Achievements

Despite the fact that RNA structural alignments have been studied for a long time, there is still a problem that the computational complexity is still large. For this reason, we cannot perform even a basic analysis of "comparing sequences" by exact methods for relatively long RNA sequences such as long non-coding RNAs and RNA viruses. In this research, we developed a fast and accurate method of calculating RNA structural alignments with consideration of complicated higher order structures such as pseudoknots by a novel algorithm based on maximizing the expected accuracy and the dual decomposition.

Free Research Field

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