Autor:

Rybarczyk, Agnieszka ; Hertz, Alain ; Kasprzak, Marta ; Blazewicz, Jacek

Współtwórca:

Korbicz, Józef (1951- ) - red. ; Uciński, Dariusz - red.

Tytuł:

Tabu search for the RNA partial degradation problem

Tytuł publikacji grupowej:

AMCS, Volume 27 (2017)

Temat i słowa kluczowe:

RNA degradation ; tabu search ; bioinformatics

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.

Wydawca:

Zielona Góra: Uniwersytet Zielonogórski

Data wydania:

2017

Typ zasobu:

artykuł

DOI:

10.1515/amcs-2017-0028

Strony:

401-415

Źródło:

AMCS, volume 27, number 2 (2017) ; kliknij tutaj, żeby przejść

Jezyk:

eng

Licencja CC BY 4.0:

kliknij tutaj, żeby przejść

Prawa do dysponowania publikacją:

Biblioteka Uniwersytetu Zielonogórskiego