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A Mathematical Analysis of RNA Structural Motifs in Viruses

Author

Listed:
  • Alexander Churkin

    (Department of Software Engineering, Sami Shamoon College of Engineering, Beer-Sheva 8410501, Israel
    Equal contribution.)

  • Franziska Totzeck

    (Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany
    Equal contribution.)

  • Rami Zakh

    (Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel)

  • Marina Parr

    (Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany)

  • Tamir Tuller

    (Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv 6997801, Israel)

  • Dmitrij Frishman

    (Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany)

  • Danny Barash

    (Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel)

Abstract

RNA stem-loop structures play an important role in almost every step of the viral replication cycle. In this contribution, a mathematical analysis is performed on a large dataset of RNA secondary structure elements in the coding regions of viruses by using topological indices that capture the Laplacian eigenvalues of the associated RNA graph representations and thereby enable structural classification, supplemented by folding energy and mutational robustness. The application of such an analysis for viral RNA structural motifs is described, being able to extract structural categories such as stem-loop structures of different sizes according to the tree-graph representation of the RNA structure, in our attempt to find novel functional motifs. While the analysis is carried on a large dataset of viral RNA structures, it can be applied more generally to other data that involve RNA secondary structures in biological agents.

Suggested Citation

  • Alexander Churkin & Franziska Totzeck & Rami Zakh & Marina Parr & Tamir Tuller & Dmitrij Frishman & Danny Barash, 2021. "A Mathematical Analysis of RNA Structural Motifs in Viruses," Mathematics, MDPI, vol. 9(6), pages 1-13, March.
    • Handle: RePEc:gam:jmathe:v:9:y:2021:i:6:p:585-:d:514005
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    Cited by:

    1. Alexander Churkin & Danny Barash, 2022. "Mathematical and Computational Biology of Viruses at the Molecular or Cellular Levels," Mathematics, MDPI, vol. 10(23), pages 1-4, November.

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