A review of di erent ways to insert known RNA modules into RNA secondary structures

Abstract : common approach to RNA folding pipelines is to start by predicting secondary structures from sequence, and then, tertiary spatial folds from the secondary structure. In this review, we are interested in a backward approach: we explore what information from known solved RNA 3D structures can be used to improve secondary structure prediction. We propose a Pareto-based method for predicting secondary structures by minimizing a bi-objective half energy-based, half knowledge-based potential. The tool outputs the sec- ondary structures from the Pareto set. We use it to compare several approaches to insert RNA modules into the secondary structures and benchmark them against the RNAstrand secondary structure database. We compare two di erent module data sources, Rna3Dmotif and The RNA Motif Atlas and di erent ways to score the module insertions taking into account module size, module complexity, or module probability according to models like JAR3D and the recent BayesPairing method.
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Submitted on : Thursday, January 9, 2020 - 10:29:08 PM
Last modification on : Saturday, January 11, 2020 - 1:23:16 AM


  • HAL Id : hal-02434317, version 1


Louis Becquey, Eric Angel, Fariza Tahi. A review of di erent ways to insert known RNA modules into RNA secondary structures. Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2019), Jul 2019, Nantes, France. ⟨hal-02434317⟩



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