Frontiers in Molecular Biosciences (Dec 2018)

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

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

DOI
https://doi.org/10.3389/fmolb.2018.00111
Journal volume & issue
Vol. 5

Abstract

Read online

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.

Keywords