Title: Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements

Authors: Yuan Li; Cuncong Zhong; Shaojie Zhang

Addresses: Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida 32816, USA ' Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida 32816, USA ' Department of Electrical Engineering and Computer Science, University of Central Florida, Orlando, Florida 32816, USA

Abstract: Many non-coding RNAs (ncRNAs) can fold into alternate native structures and perform different biological functions. The computational prediction of an ncRNA's alternate native structures can be conducted by analysing the ncRNA's energy landscape. Previously, we have developed a computational approach, RNASLOpt, to predict alternate native structures for a single RNA. In this paper, in order to improve the accuracy of the prediction, we incorporate structural conservation information among a family of related ncRNA sequences to the prediction. We propose a comparative approach, RNAConSLOpt, to produce all possible consensus SLOpt stack configurations that are conserved on the consensus energy landscape of a family of related ncRNAs. Benchmarking tests show that RNAConSLOpt can reduce the number of candidate structures compared with RNASLOpt, and can predict ncRNAs' alternate native structures accurately. Moreover, an application of the proposed pipeline to bacteria in Bacillus genus has discovered several novel riboswitch candidates.

Keywords: bioinformatics; RNA consensus secondary structures; RNA energy landscape; RNA stable local optimal structure; riboswitch; RNA sequence alignment; non-coding RNAs; ncRNA sequences; bacteria; Bacillus genus.

DOI: 10.1504/IJBRA.2014.062997

International Journal of Bioinformatics Research and Applications, 2014 Vol.10 No.4/5, pp.498 - 518

Published online: 24 Oct 2014 *

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