Work

Algorithms for ranking and unranking the combinatorial set of RNA secondary structures

Year: 2025

Type: article

Abstract: In this paper, we study the combinatorial set of RNA secondary structures. The main contribution of this paper is the developed ranking and unranking algorithms for the combinatorial set of pseudoknot-free RNA secondary structures of length [Formula: see text] with [Formula: see text] base-pairs. The developed algorithms are based on a bijection between the set of RNA structures and the variants of the corresponding AND/OR tree structure. Assuming a unit-cost RAM model, the developed algorithms have polynomial time complexity [Formula: see text] for [Formula: see text] and [Formula: see text] for [Formula: see text]. In contrast to the existing algorithms, the new algorithms do not require preprocessing steps and have better overall time complexity.

Source: Discrete Mathematics Algorithms and Applications

DOI: 10.1142/s1793830925500594

Authors: Yuriy Shablya, Dmitry Kruchinin

Institutions: Tomsk State University of Control Systems and Radio-Electronics, Sirius University of Science and Technology

Language: English

Topic: RNA and protein synthesis mechanisms

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: Russian Foundation for Basic Research, Russian Science Foundation

Awards: G3747393151, G8662287124