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Bioinformatics Advance Access originally published online on February 26, 2009
Bioinformatics 2009 25(9):1137-1144; doi:10.1093/bioinformatics/btp110
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

A robust peak detection method for RNA structure inference by high-throughput contact mapping

Jinkyu Kim 1, Seunghak Yu 1, Byonghyo Shim 2, Hanjoo Kim 1, Hyeyoung Min 3, Eui-Young Chung 4, Rhiju Das 5 and Sungroh Yoon 1,*

1School of Electrical Engineering, 2Department of Computer Science, Korea University, Seoul 136-713, Korea, 3College of Pharmacy, Chung-Ang University, Seoul 156-756, Korea, 4Department of Electrical and Electronic Engineering, Yonsei University, Seoul 120-749, Korea and 5Departments of Biochemistry and Physics, Stanford University, Stanford, CA 94305, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: For high-throughput prediction of the helical arrangements of large RNA molecules, an innovative method termed multiplexed hydroxyl radical (·OH) cleavage analysis (MOHCA) has been proposed. A key step in this promising technique is to detect peaks accurately from noisy radioactivity profiles. Since manual peak finding is laborious and prone to error, an automated peak detection method to improve the accuracy and throughput of MOHCA is required. Existing methods were not applicable to MOHCA due to their high false positive rates.

Results: We developed a two-step computational method that can detect peaks from MOHCA profiles in a robust manner. The first step exploits an ensemble of linear and non-linear signal processing techniques to find true peak candidates. In the second step, a binary classifier trained with the characteristics of true and false peaks is used to eliminate false peaks out of the peak candidates. We tested the proposed approach with 2002 MOHCA cleavage profiles and obtained the median recall, precision and F-measure values of 0.917, 0.750 and 0.830, respectively. Compared with the alternatives considered, the proposed method was able to handle false peaks substantially better, thus resulting in 51.0–71.8% higher median values of precision and F-measure.

Availability: The software and supplementary data are available at http://dna.korea.ac.kr/pub/mohca

Contact: sryoon{at}korea.ac.kr

Associate Editor: Anna Tramontano

Received on November 18, 2008; revised on January 30, 2009; accepted on February 22, 2009

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