Estimating the power of sequence covariation for detecting conserved RNA structure.

Abstract

Pairwise sequence covariations are a signal of conserved RNA secondary structure. We describe a method for distinguishing when lack of covariation signal can be taken as evidence against a conserved RNA structure, as opposed to when a sequence alignment merely has insufficient variation to detect covariations. We find that alignments for several long non-coding RNAs previously shown to lack covariation support do have adequate covariation detection power, providing additional evidence against their proposed conserved structures. The R-scape web server is at eddylab.org/R-scape, with a link to download the source code. Supplementary data are available at Bioinformatics online.