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New models and algorithms for RNA pseudoknot order assignment

Zok Tomasz, Badura Jan, Swat Sylwester, Figurski Kacper, Popenda Mariusz, Antczak Maciej

International Journal of Applied Mathematics and Computer Science

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2020

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Vol. 30, no. 2

315--324

EN

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.

2

On parameters of independence, domination and irredundance in edge-coloured graphs and their products

Włoch A., Włoch I.

Journal of Mathematics and Applications

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2012

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Vol. 35

97--106

EN

In this paper we study some parameters of domination, independence and irredundance in some edge-coloured graphs and their products. We present several general properties of independent, dominating and irredundance sets in edge-coloured graphs and we give relationships between the independence, domination and irredundant numbers of an edge-coloured graph. We generalize some classical results concerning independence, domination and irredundance in graphs. Moreover we study G-join of edge-coloured graphs which preserves considered parameters with respect to related parameters in product factors.

3

On k-independent sets and (k, l)-kernels in the corona of graphs

Szumny W., Włoch A.

Journal of Mathematics and Applications

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2007

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Vol. 29

127-135

EN

A subset S ⊆ V(G) is a k-independent set if no two of its vertices are in distance less than k. In this paper we study fc-independent sets and (k, l)-kernels (i.e. k-independent sets being l-dominating simultaneously) in the corona of graphs. We describe an arbitrary k-independent set of the corona and next we determine the Fibonacci number and the generalized Fibonacci number of the corona of special graphs. We give the necessary and sufficient conditions for the existence of (k, l)-kernels in the corona.