Introduction

Many functional RNAs have an evolutionarily conserved secondary structure. Conservation of RNA base pairing induces pairwise covariations in sequence alignments. We developed a computational method, R-scape (RNA Structural Covariation Above Phylogenetic Expectation), that quantitatively tests whether covariation analysis supports the presence of a conserved RNA secondary structure. R-scape analysis finds no statistically significant support for proposed secondary structures of the long noncoding RNAs HOTAIR, SRA, and Xist.

Publications

  1. A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.
    Cite this
    Rivas E, Clements J, Eddy SR, 2017-01-01 - Nature methods

Credits

  1. Elena Rivas
    Developer

    Department of Molecular and Cellular Biology, Harvard University, United States of America

  2. Jody Clements
    Developer

    Janelia Research Campus, Howard Hughes Medical Institute, United States of America

  3. Sean R Eddy
    Investigator

    John A. Paulson School of Engineering and Applied Sciences, Harvard University, United States of America

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Summary
AccessionBT007047
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted BySean R Eddy