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Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction

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Bioinformatics Research and Applications (ISBRA 2023)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 14248))

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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.

This work was funded by the Deutsche Forschungsgemeinschaft (DFG grant number STA 850/48-1) and by the Austrian Science Fund (FWF grant number F-80 and I-4520).

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Notes

  1. 1.

    https://github.com/ViennaRNA/ViennaRNA/blob/master/src/Utils/refold.pl.

  2. 2.

    www.bioinf.uni-leipzig.de/publications/supplements/23-002.

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Author information

Authors and Affiliations

  1. Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, 04107, Leipzig, Germany

    Sarah von Löhneysen & Peter F. Stadler

  2. Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria

    Thomas Spicher, Yuliia Varenyk, Hua-Ting Yao, Ronny Lorenz, Ivo Hofacker & Peter F. Stadler

  3. Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany

    Peter F. Stadler

  4. Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia

    Peter F. Stadler

  5. Santa Fe Institute, Santa Fe, NM, USA

    Peter F. Stadler

  6. UniVie Doctoral School Computer Science (DoCS), University of Vienna, Währinger Str. 29, 1090, Vienna, Austria

    Thomas Spicher

  7. Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria

    Yuliia Varenyk

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  1. Sarah von Löhneysen
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  2. Thomas Spicher
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Corresponding author

Correspondence to Peter F. Stadler .

Editor information

Editors and Affiliations

  1. University of North Texas, Denton, TX, USA

    Xuan Guo

  2. University of Southern California, Los Angeles, CA, USA

    Serghei Mangul

  3. Georgia State University, Atlanta, GA, USA

    Murray Patterson

  4. Georgia State University, Atlanta, GA, USA

    Alexander Zelikovsky

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© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

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von Löhneysen, S. et al. (2023). Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction. In: Guo, X., Mangul, S., Patterson, M., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2023. Lecture Notes in Computer Science(), vol 14248. Springer, Singapore. https://doi.org/10.1007/978-981-99-7074-2_21

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  • DOI: https://doi.org/10.1007/978-981-99-7074-2_21

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