Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures

J Mol Biol. 2019 Apr 5;431(8):1592-1603. doi: 10.1016/j.jmb.2019.03.012. Epub 2019 Mar 16.


The existence of evolutionary conservation in base pairing is strong evidence for functional elements of RNA structure, although available tools for rigorous identification of structural conservation are limited. R-scape is a recently developed program for statistical prediction of pairwise covariation from sequence alignments, but it initially showed limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for a more powerful analysis of structure conservation in long RNA molecules, including mammalian lncRNAs.

Keywords: RNAalifold; conserved structure; covariation analysis; lncRNA structure; long non-coding RNAs.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Conserved Sequence
  • Evolution, Molecular
  • Humans
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA, Long Noncoding / chemistry
  • RNA, Long Noncoding / genetics*


  • RNA, Long Noncoding