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Updated: Dec 29, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
Published on: December 9, 2022
Estimating the power of sequence covariation for detecting conserved RNA structure
Elena Rivas1, Jody Clements2, Sean R Eddy1,3,4
1Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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.
Availability And Implementation:
The R-scape web server is at eddylab.org/R-scape, with a link to download the source code.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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