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Open Access

A Novel Structural Measure Separating Non-Coding RNAs from Genomic Backgrounds

School of Information Technology, Middle Georgia State University, Macon, GA 31206, USA.
Department of Plant Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
Department of Computer Science and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.
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Abstract

RNA secondary structure has become the most exploitable feature for ab initio detection of non-coding RNA (ncRNA) genes from genome sequences. Previous work has used Minimum Free Energy (MFE) based methods developed to identify ncRNAs by measuring sequence fold stability and certainty. However, these methods yielded variable performances across different ncRNA species. Designing novel reliable structural measures will help to develop effective ncRNA gene finding tools. This paper introduces a new RNA structural measure based on a novel RNA secondary structure ensemble constrained by characteristics of native RNA tertiary structures. The new method makes it possible to achieve a performance leap from the previous structure-based methods. Test results on standard ncRNA datasets (benchmarks) demonstrate that this method can effectively separate most ncRNAs families from genome backgrounds.

Keywords

RNA secondary structureRNA tertiary structureInside algorithm

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Tsinghua Science and Technology
Volume 20 Issue 5,
October 2015
Pages 474-483
DOI: 10.1109/TST.2015.7297746
Cite this article:
Wang Y, Malmberg RL, Cai L. A Novel Structural Measure Separating Non-Coding RNAs from Genomic Backgrounds. Tsinghua Science and Technology, 2015, 20(5): 474-483. https://doi.org/10.1109/TST.2015.7297746

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Received: 24 June 2015
Accepted: 24 July 2015
Published: 13 October 2015
The author(s) 2015
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