Tabu search for the RNA partial degradation problem

Rybarczyk, A.; Hertz, A.; Kasprzak, M.; Blazewicz, J.

doi:10.1515/amcs-2017-0028

Artykuł - szczegóły

Tytuł artykułu

Tabu search for the RNA partial degradation problem

Autorzy

Rybarczyk A. , Hertz A. , Kasprzak M. , Blazewicz J.

Treść / Zawartość

Pełne teksty:

13_rybarczyk_hertz_kasprzak_tabu_search_2017_2.pdf

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Identyfikatory

DOI

10.1515/amcs-2017-0028

Warianty tytułu

Języki publikacji

Abstrakty

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.

Słowa kluczowe

RNA degradation tabu search bioinformatics

rozkład RNA algorytm tabu search bioinformatyka

Wydawca

Oficyna Wydawnicza Uniwersytetu Zielonogórskiego

Czasopismo

International Journal of Applied Mathematics and Computer Science

Rocznik

2017

Tom

Vol. 27, no. 2

Strony

401--415

Opis fizyczny

Bibliogr. 33 poz., tab., wykr.

Twórcy

autor

Rybarczyk A.

Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznan, Poland

autor

Hertz A.

Department of Mathematics and Industrial Engineering, Polytechnique Montreal/GERAD, Montreal, Canada

autor

Kasprzak M.

Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznan, Poland

autor

Blazewicz J.

jblazewicz@cs.put.poznan.pl

Institute of Computing Science, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12, 61-704 Poznan, Poland

Bibliografia

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Uwagi

Opracowanie ze środków MNiSW w ramach umowy 812/P-DUN/2016 na działalność upowszechniającą naukę (zadania 2017).

Typ dokumentu

Bibliografia

Identyfikator YADDA

bwmeta1.element.baztech-5387223b-199e-4aec-a4a0-de9849c9f461