AUTHOR=Delli Ponti Riccardo , Armaos Alexandros , Marti Stefanie , Tartaglia Gian Gaetano 

TITLE=A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=5

YEAR=2018

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2018.00111

DOI=10.3389/fmolb.2018.00111

ISSN=2296-889X

ABSTRACT=<p>To compare the secondary structure profiles of RNA molecules we developed the <italic>CROSSalign</italic> method. <italic>CROSSalign</italic> 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 <italic>CROSSalign</italic> to investigate the structural conservation of long non-coding RNAs such as <italic>XIST</italic> and <italic>HOTAIR</italic> as well as ssRNA viruses including <italic>HIV</italic>. <italic>CROSSalign</italic> 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 <italic>CROSSalign</italic> accurately recognizes repeat A of <italic>XIST</italic> and domain D2 of <italic>HOTAIR</italic> and outperforms other methods based on covariance modeling. The algorithm is freely available at the webpage <ext-link ext-link-type="uri" xlink:href="http://service.tartaglialab.com//new_submission/crossalign" xmlns:xlink="http://www.w3.org/1999/xlink">http://service.tartaglialab.com//new_submission/crossalign</ext-link>.</p>