<abstract xmlns="http://www.w3.org/1999/xhtml"><p>The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment, interact with each other and form base pairs. Pseudoknots are characterized by great topological diversity, and their systematic description is still a challenge. In our previous work, we have introduced the <italic>pseudoknot order</italic>: a new coefficient representing the topological complexity of the pseudoknotted RNA structure. It is defined as the minimum number of base pair set decompositions, aimed to obtain the unknotted RNA structure. We have suggested how it can be useful in the interpretation and understanding of a hierarchy of RNA folding. However, it is not trivial to unambiguously identify pseudoknots and determine their orders in an RNA structure. Therefore, since the introduction of this coefficient, we have worked on the method to reliably assign pseudoknot orders in correspondence to the mechanisms that control the biological process leading to their formation in the molecule. Here, we introduce a novel graph coloring-based model for the problem of pseudoknot order assignment. We show a specialized heuristic operating on the proposed model and an alternative integer programming algorithm. The performance of both approaches is compared with that of state-of-the-art algorithms which so far have been most efficient in solving the problem in question. We summarize the results of computational experiments that evaluate our new methods in terms of classification quality on a representative data set originating from the non-redundant RNA 3D structure repository.</p></abstract>

The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment, interact with each other and form base pairs. Pseudoknots are characterized by great topological diversity, and their systematic description is still a challenge. In our previous work, we have introduced the pseudoknot order: a new coefficient representing the topological complexity of the pseudoknotted RNA structure. It is defined as the minimum number of base pair set decompositions, aimed to obtain the unknotted RNA structure. We have suggested how it can be useful in the interpretation and understanding of a hierarchy of RNA folding. However, it is not trivial to unambiguously identify pseudoknots and determine their orders in an RNA structure. Therefore, since the introduction of this coefficient, we have worked on the method to reliably assign pseudoknot orders in correspondence to the mechanisms that control the biological process leading to their formation in the molecule. Here, we introduce a novel graph coloring-based model for the problem of pseudoknot order assignment. We show a specialized heuristic operating on the proposed model and an alternative integer programming algorithm. The performance of both approaches is compared with that of state-of-the-art algorithms which so far have been most efficient in solving the problem in question. We summarize the results of computational experiments that evaluate our new methods in terms of classification quality on a representative data set originating from the non-redundant RNA 3D structure repository.

New models and algorithms for RNA pseudoknot order assignment

International Journal of Applied Mathematics and Computer Science

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

{"article-title":"New models and algorithms for RNA pseudoknot order assignment"}

The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two...

New models and algorithms for RNA pseudoknot order assignment

Online veröffentlicht: 04. Juli 2020

Seitenbereich: 315 - 324

Eingereicht: 25. Juli 2019

Akzeptiert: 12. März 2020

DOI: https://doi.org/10.34768/amcs-2020-0024

Schlüsselwörter
RNA pseudoknot order, conflict graph, vertex coloring, maximum independent set, integer programming

© 2020 Tomasz Zok et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

New models and algorithms for RNA pseudoknot order assignment

Online veröffentlicht: 04. Juli 2020

Seitenbereich: 315 - 324

Eingereicht: 25. Juli 2019

Akzeptiert: 12. März 2020

DOI: https://doi.org/10.34768/amcs-2020-0024

SchlüsselwörterRNA pseudoknot order, conflict graph, vertex coloring, maximum independent set, integer programming

© 2020 Tomasz Zok et al., published by Sciendo

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Schlüsselwörter
RNA pseudoknot order, conflict graph, vertex coloring, maximum independent set, integer programming