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 biological systems. They not only serve as templates in protein synthesis or as adapters in the translation process, but also influence and are...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Sciendo
2017-06-01
|
Series: | International Journal of Applied Mathematics and Computer Science |
Subjects: | |
Online Access: | https://doi.org/10.1515/amcs-2017-0028 |
id |
doaj-deba97e50f094238be824e0c0ab75e91 |
---|---|
record_format |
Article |
spelling |
doaj-deba97e50f094238be824e0c0ab75e912021-09-06T19:39:50ZengSciendoInternational Journal of Applied Mathematics and Computer Science2083-84922017-06-0127240141510.1515/amcs-2017-0028amcs-2017-0028Tabu Search for the RNA Partial Degradation ProblemRybarczyk Agnieszka0Hertz Alain1Kasprzak Marta2Blazewicz Jacek3Institute of Computing Science Poznan University of Technology, Piotrowo 2, 60-965 Poznan, PolandDepartment of Mathematics and Industrial Engineering Polytechnique Montreal/GERAD, Montreal, CanadaInstitute of Computing Science Poznan University of Technology, Piotrowo 2, 60-965 Poznan, PolandInstitute of Computing Science Poznan University of Technology, Piotrowo 2, 60-965 Poznan, PolandIn 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.https://doi.org/10.1515/amcs-2017-0028rna degradationtabu searchbioinformatics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Rybarczyk Agnieszka Hertz Alain Kasprzak Marta Blazewicz Jacek |
spellingShingle |
Rybarczyk Agnieszka Hertz Alain Kasprzak Marta Blazewicz Jacek Tabu Search for the RNA Partial Degradation Problem International Journal of Applied Mathematics and Computer Science rna degradation tabu search bioinformatics |
author_facet |
Rybarczyk Agnieszka Hertz Alain Kasprzak Marta Blazewicz Jacek |
author_sort |
Rybarczyk Agnieszka |
title |
Tabu Search for the RNA Partial Degradation Problem |
title_short |
Tabu Search for the RNA Partial Degradation Problem |
title_full |
Tabu Search for the RNA Partial Degradation Problem |
title_fullStr |
Tabu Search for the RNA Partial Degradation Problem |
title_full_unstemmed |
Tabu Search for the RNA Partial Degradation Problem |
title_sort |
tabu search for the rna partial degradation problem |
publisher |
Sciendo |
series |
International Journal of Applied Mathematics and Computer Science |
issn |
2083-8492 |
publishDate |
2017-06-01 |
description |
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. |
topic |
rna degradation tabu search bioinformatics |
url |
https://doi.org/10.1515/amcs-2017-0028 |
work_keys_str_mv |
AT rybarczykagnieszka tabusearchforthernapartialdegradationproblem AT hertzalain tabusearchforthernapartialdegradationproblem AT kasprzakmarta tabusearchforthernapartialdegradationproblem AT blazewiczjacek tabusearchforthernapartialdegradationproblem |
_version_ |
1717769950429446144 |