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Título:	A method for RNA structure prediction shows evidence for structure in lncRNAs
Autor/a:	Delli Ponti, Riccardo, 1987-; Armaos, Alexandros; Marti, Stefanie; Tartaglia, Gian Gaetano
Abstract:	To compare the secondary structure profiles of RNA molecules we developed the CROSSalign method. CROSSalign is based on the combination of the Computational Recognition Of Secondary Structure (CROSS) algorithm to predict the RNA secondary structure profile at single-nucleotide resolution and the Dynamic Time Warping (DTW) method to align profiles of different lengths. We applied CROSSalign to investigate the structural conservation of long non-coding RNAs such as XIST and HOTAIR as well as ssRNA viruses including HIV. CROSSalign performs pair-wise comparisons and is able to find homologs between thousands of matches identifying the exact regions of similarity between profiles of different lengths. In a pool of sequences with the same secondary structure CROSSalign accurately recognizes repeat A of XIST and domain D2 of HOTAIR and outperforms other methods based on covariance modeling. The algorithm is freely available at the webpage http://service.tartaglialab.com//new_submission/crossalign.
Abstract:	The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007–2013), through the European Research Council, under grant agreement RIBOMYLOME_309545 (Gian Gaetano Tartaglia), and from the Spanish Ministry of Economy and Competitiveness (BFU2014-55054-P and BFU2017-86970-P). We also acknowledge support from AGAUR (2014 SGR 00685), the Spanish Ministry of Economy and Competitiveness, Centro de Excelencia Severo Ochoa 2013–2017 (SEV-2012-0208). We also thank the CRG fellowship to SM.
Materia(s):	-Non-coding RNA -Secondary structure -Structural alignments -Pair-wise comparisons -Sequence-based predictions -RNA evolution
Derechos:	© 2018 Delli Ponti, Armaos, Marti and Tartaglia. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY) (http://creativecommons.org/licenses/by/4.0/). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. http://creativecommons.org/licenses/by/4.0/
Tipo de documento:	Artículo Artículo - Versión publicada
Editor:	Frontiers
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