Tabu Search for the RNA Partial Degradation Problem

Abstract

In recent years, a growing interest has been observed in research on RNA (ribonucleic acid), primarily due to the discovery of the role of RNA molecules in biological systems. They not only serve as templates in protein synthesis or as adapters in the translation process, but also influence and are involved in the regulation of gene expression. The RNA degradation process is now heavily studied as a potential source of such riboregulators. In this paper, we consider the so-called RNA partial degradation problem (RNA PDP). By solving this combinatorial problem, one can reconstruct a given RNA molecule, having as input the results of the biochemical analysis of its degradation, which possibly contain errors (false negatives or false positives). From the computational point of view the RNA PDP is strongly NP-hard. Hence, there is a need for developing algorithms that construct good suboptimal solutions. We propose a heuristic approach, in which two tabu search algorithms cooperate, in order to reconstruct an RNA molecule. Computational tests clearly demonstrate that the proposed approach fits well the biological problem and allows to achieve near-optimal results. The algorithm is freely available at http://www.cs.put.poznan.pl/arybarczyk/tabusearch.php.

Multi-agent approach to sequence structure simulation in the RNA World hypothesis

“…As a continuation of the research reported in this paper, one may consider taking into account the exact RNA replication mechanism as described in [61]. Additionally, in order to reflect more accurately the RNA folding and what follows, the interactions between RNA molecules, one may consider extended secondary (taking into account both canonical and noncanonical base pairs contrary to 2D structure which considers canonical base pairs only) and tertiary interactions (formed between secondary structure elements and constituting RNA tertiary (3D) structure) within and between RNA chains [62][63][64][65][66]. However, conducting such simulations will certainly require very high computing power.…”

New models and algorithms for RNA pseudoknot order assignment

“…For example, structural motifs can be searched for in a sequence (i.e., a primary structure), in an intramolecular interaction network (i.e., a secondary structure), or in a full-atom 3D model (i.e., a tertiary structure). Their reliable identification and analysis often bring significant insight into the understanding of biological processes (Rybarczyk et al, 2017). Structural motifs play various important biological roles, e.g., serving as binding sites in molecular complexes, indicating cleavage sites in the biogenesis of specialized molecules, blocking or initiating some cellular processes, etc.…”