<abstract xmlns="http://www.w3.org/1999/xhtml"><p> 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.</p></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.

Tabu Search for the RNA Partial Degradation Problem

International Journal of Applied Mathematics and Computer Science

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

{"article-title":"Tabu Search for the RNA Partial Degradation Problem"}

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...

Tabu Search for the RNA Partial Degradation Problem

Published Online: Jul 08, 2017

Page range: 401 - 415

Received: Oct 24, 2016

Accepted: Feb 15, 2017

DOI: https://doi.org/10.1515/amcs-2017-0028

Keywords
RNA degradation, tabu search, bioinformatics

© by Jacek Blazewicz

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

Tabu Search for the RNA Partial Degradation Problem

Published Online: Jul 08, 2017

Page range: 401 - 415

Received: Oct 24, 2016

Accepted: Feb 15, 2017

DOI: https://doi.org/10.1515/amcs-2017-0028

KeywordsRNA degradation, tabu search, bioinformatics

© by Jacek Blazewicz

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

Keywords
RNA degradation, tabu search, bioinformatics