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Covariation analysis with improved parameters reveals conservation in lncRNA structures

Rafael C A Tavares, Anna Marie Pyle, Srinivas Somarowthu
doi: https://doi.org/10.1101/364109
Rafael C A Tavares
1Department of Chemistry, Yale University, New Haven, Connecticut, USA
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Anna Marie Pyle
1Department of Chemistry, Yale University, New Haven, Connecticut, USA
2Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
3Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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Srinivas Somarowthu
4Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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Abstract

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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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted July 06, 2018.
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Covariation analysis with improved parameters reveals conservation in lncRNA structures
Rafael C A Tavares, Anna Marie Pyle, Srinivas Somarowthu
bioRxiv 364109; doi: https://doi.org/10.1101/364109
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Covariation analysis with improved parameters reveals conservation in lncRNA structures
Rafael C A Tavares, Anna Marie Pyle, Srinivas Somarowthu
bioRxiv 364109; doi: https://doi.org/10.1101/364109

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