Covariation analysis with improved parameters reveals conservation in lncRNA structures
The existence of phylogenetic covariation in base-pairing is strong evidence for functional elements of RNA structure, although available tools for identifying covariation are limited. R-scape is a recently developed program for prediction of covariation from sequence alignments, but it has limited utility on long RNAs, especially those of eukaryotic origin. Here we show that R-scape can be adapted for powerful prediction of covariation in long RNA molecules, including mammalian lncRNAs.
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