A method for RNA structure prediction shows evidence for structure in lncRNAs

Ponti, Riccardo Delli; Armaos, Alexandros; Marti, Stefanie; Tartaglia, Gian Gaetano

To compare the secondary structure 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 at single-nucleotide resolution using sequence information only 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. The algorithm is able to find homologues between thousands of possible matches identifying the exact regions of similarity between profiles of different length. CROSSalign is freely available at the webpage http://service.tartaglialab.com//new_submission/crossalign.