A Mathematical Analysis of RNA Structural Motifs in Viruses
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 Laplac...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-03-01
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| Series: | Mathematics |
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| Online Access: | https://www.mdpi.com/2227-7390/9/6/585 |
| _version_ | 1797542020003135488 |
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| author | Alexander Churkin Franziska Totzeck Rami Zakh Marina Parr Tamir Tuller Dmitrij Frishman Danny Barash |
| author_facet | Alexander Churkin Franziska Totzeck Rami Zakh Marina Parr Tamir Tuller Dmitrij Frishman Danny Barash |
| author_sort | Alexander Churkin |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T13:23:43Z |
| format | Article |
| id | doaj.art-ebe6142140624131983d08f63ac36b80 |
| institution | Directory Open Access Journal |
| issn | 2227-7390 |
| language | English |
| last_indexed | 2024-03-10T13:23:43Z |
| publishDate | 2021-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Mathematics |
| spelling | doaj.art-ebe6142140624131983d08f63ac36b802023-11-21T09:50:52ZengMDPI AGMathematics2227-73902021-03-019658510.3390/math9060585A Mathematical Analysis of RNA Structural Motifs in VirusesAlexander Churkin0Franziska Totzeck1Rami Zakh2Marina Parr3Tamir Tuller4Dmitrij Frishman5Danny Barash6Department of Software Engineering, Sami Shamoon College of Engineering, Beer-Sheva 8410501, IsraelDepartment of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, GermanyDepartment of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, IsraelDepartment of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, GermanyDepartment of Biomedical Engineering, Tel-Aviv University, Tel-Aviv 6997801, IsraelDepartment of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, GermanyDepartment of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, IsraelRNA 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.https://www.mdpi.com/2227-7390/9/6/585RNA graph representationLaplacian eigenvaluestopological indicesfolding energymutational robustness |
| spellingShingle | Alexander Churkin Franziska Totzeck Rami Zakh Marina Parr Tamir Tuller Dmitrij Frishman Danny Barash A Mathematical Analysis of RNA Structural Motifs in Viruses Mathematics RNA graph representation Laplacian eigenvalues topological indices folding energy mutational robustness |
| title | A Mathematical Analysis of RNA Structural Motifs in Viruses |
| title_full | A Mathematical Analysis of RNA Structural Motifs in Viruses |
| title_fullStr | A Mathematical Analysis of RNA Structural Motifs in Viruses |
| title_full_unstemmed | A Mathematical Analysis of RNA Structural Motifs in Viruses |
| title_short | A Mathematical Analysis of RNA Structural Motifs in Viruses |
| title_sort | mathematical analysis of rna structural motifs in viruses |
| topic | RNA graph representation Laplacian eigenvalues topological indices folding energy mutational robustness |
| url | https://www.mdpi.com/2227-7390/9/6/585 |
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