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Detecting and Comparing Non-Coding RNAs in the High-Throughput Era
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Bioinformatics and Genomics Program, Centre for Genomic Regulation (CRG), Aiguader, 88, 08003 Barcelona, Spain
* Author to whom correspondence should be addressed.
Received: 31 May 2013; in revised form: 16 July 2013 / Accepted: 17 July 2013 / Published: 24 July 2013
Abstract: In recent years there has been a growing interest in the field of non-coding RNA. This surge is a direct consequence of the discovery of a huge number of new non-coding genes and of the finding that many of these transcripts are involved in key cellular functions. In this context, accurately detecting and comparing RNA sequences has become important. Aligning nucleotide sequences is a key requisite when searching for homologous genes. Accurate alignments reveal evolutionary relationships, conserved regions and more generally any biologically relevant pattern. Comparing RNA molecules is, however, a challenging task. The nucleotide alphabet is simpler and therefore less informative than that of amino-acids. Moreover for many non-coding RNAs, evolution is likely to be mostly constrained at the structural level and not at the sequence level. This results in very poor sequence conservation impeding comparison of these molecules. These difficulties define a context where new methods are urgently needed in order to exploit experimental results to their full potential. This review focuses on the comparative genomics of non-coding RNAs in the context of new sequencing technologies and especially dealing with two extremely important and timely research aspects: the development of new methods to align RNAs and the analysis of high-throughput data.
Keywords: lncRNAs; ncRNAs; high-throughput; RNA-seq; comparative biology; sequencing
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Bussotti, G.; Notredame, C.; Enright, A.J. Detecting and Comparing Non-Coding RNAs in the High-Throughput Era. Int. J. Mol. Sci. 2013, 14, 15423-15458.
Bussotti G, Notredame C, Enright AJ. Detecting and Comparing Non-Coding RNAs in the High-Throughput Era. International Journal of Molecular Sciences. 2013; 14(8):15423-15458.
Bussotti, Giovanni; Notredame, Cedric; Enright, Anton J. 2013. "Detecting and Comparing Non-Coding RNAs in the High-Throughput Era." Int. J. Mol. Sci. 14, no. 8: 15423-15458.