Prediction of sequentially optimal RNA secondary structures
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Updated: Nov 1, 2026

RNA Secondary Structure Prediction Using High-throughput SHAPE
Published on: May 31, 2013
N Breton1, C Jacob, P Daegelen
1I.N.R.A. Laboratoire de Biometrie, Institut National de la Recherche Agronomique, Jouy-en-Josas, France.
Abstract:
A rigorous mathematical modeling of the RNA sequential folding process during transcription is proposed. It is based, at each transcription step, on a homogeneous markovian jump process, the state space of which is the set of structures constructible on the part of the RNA already transcribed. A theoretical formula permitting the computation of the structures probabilities at the end of the RNA transcription is derived. Successive approximations, aimed at reducing the size of the state space, permit the design of a prediction algorithm. The algorithm is tested on some structural RNAs (tRNA, 5S, 16S, hammerhead, ...), results are discussed and possible improvements are proposed.
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