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2023 | OriginalPaper | Buchkapitel

Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction

verfasst von : Sarah von Löhneysen, Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo Hofacker, Peter F. Stadler

Erschienen in: Bioinformatics Research and Applications

Verlag: Springer Nature Singapore

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Abstract

Pseudo-energies are a generic method to incorporate extrinsic information into energy-directed RNA secondary structure predictions. Consensus structures of RNA families, usually predicted from multiple sequence alignments, can be treated as soft constraints in this manner. In this contribution we first revisit the theoretical framework and then show that pseudo-energies for the centroid base pairs of the consensus structure result in a substantial increase in folding accuracy. In contrast, only a moderate improvement can be achieved if only the information that a base is predominantly paired is utilized.

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Titel: Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
verfasst von: Sarah von Löhneysen
Thomas Spicher
Yuliia Varenyk
Hua-Ting Yao
Ronny Lorenz
Ivo Hofacker
Peter F. Stadler
Verlag: Springer Nature Singapore
Buch: Bioinformatics Research and Applications
Print ISBN: 978-981-9970-73-5

Electronic ISBN: 978-981-9970-74-2

Copyright-Jahr: 2023
DOI: https://doi.org/10.1007/978-981-99-7074-2_21

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