Delli Ponti, Riccardo, 1987-Armaos, Alexandros, 1989-Marti, StefanieTartaglia, Gian Gaetano2019-11-192019-11-192018Delli Ponti R, Armaos A, Marti S, Tartaglia GG. A method for RNA structure prediction shows evidence for structure in lncRNAs. Front Mol Biosci. 2018;5:111. DOI: 10.3389/fmolb.2018.001112296-889Xhttp://hdl.handle.net/10230/42886To 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.application/pdfeng© 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.info:eu-repo/semantics/articlehttp://dx.doi.org/10.3389/fmolb.2018.00111Non-coding RNASecondary structureStructural alignmentsPair-wise comparisonsSequence-based predictionsRNA evolutioninfo:eu-repo/semantics/openAccess