Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

Background: In recent years, the number of available RNA structures has rapidly grown reflecting the increased interest on RNA biology. Similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in RNA. Results: Here we introduce an all-against-all sequence- and three-dimensional (3D) structure-based comparison of a representative set of RNA structures, which have allowed us to quantitatively confirm that: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure than sequence, and (iii) there is a twilight zone for RNA homology detection. Discussion: The computational analysis here presented quantitatively describes the relationship between seque...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Emidio Capriotti, Marc A. Martí-Renom
• Keywords: BMCBI 2010, RNA Homology, RNA Molecules, Rna Structure