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    Wyświetlanie 1-5 z 5
    Tytuł:
    Some remarks on evaluating the quality of the multiple sequence alignment based on the BAliBASE benchmark
    Autorzy:
    Błażewicz, J.
    Formanowicz, P.
    Wojciechowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/930013.pdf
    Data publikacji:
    2009
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    dostosowanie odniesienia
    dokładność ustawienia
    multiple sequence alignment
    reference alignment
    alignment accuracy
    Opis:
    BAliBASE is one of the most widely used benchmarks for multiple sequence alignment programs. The accuracy of alignment methods is measured by bali score-an application provided together with the database. The standard accuracy measures are the Sum of Pairs (SP) and the Total Column (TC). We have found that, for non-core block columns, results calculated by bali score are different from those obtained on the basis of the formal definitions of the measures. We do not claim that one of these measures is better than the other, but they are definitely different. Such a situation can be the source of confusion when alignments obtained using various methods are compared. Therefore, we propose a new nomenclature for the measures of the quality of multiple sequence alignments to distinguish which one was actually calculated. Moreover, we have found that the occurrence of a gap in some column in the first sequence of the reference alignment causes column discarding.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2009, 19, 4; 675-678
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Tabu search for the RNA partial degradation problem
    Autorzy:
    Rybarczyk, A.
    Hertz, A.
    Kasprzak, M.
    Blazewicz, J.
    Powiązania:
    https://bibliotekanauki.pl/articles/330324.pdf
    Data publikacji:
    2017
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    RNA degradation
    tabu search
    bioinformatics
    rozkład RNA
    algorytm tabu search
    bioinformatyka
    Opis:
    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.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2017, 27, 2; 401-415
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Internet shopping optimization problem
    Autorzy:
    Błażewicz, J.
    Kovalyov, M. Y.
    Musiał, J.
    Urbański, A. P.
    Wojciechowski, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/907755.pdf
    Data publikacji:
    2010
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    algorytm
    złożoność obliczeniowa
    algorytm kombinatoryczny
    optymalizacja
    zakupy internetowe
    algorithm
    computational complexity
    combinatorial algorithms
    optimization
    Internet shopping
    Opis:
    A high number of Internet shops makes it difficult for a customer to review manually all the available offers and select optimal outlets for shopping. A partial solution to the problem is brought by price comparators which produce price rankings from collected offers. However, their possibilities are limited to a comparison of offers for a single product requested by the customer. The issue we investigate in this paper is a multiple-item multiple-shop optimization problem, in which total expenses of a customer to buy a given set of items should be minimized over all available offers. In this paper, the Internet Shopping Optimization Problem (ISOP) is defined in a formal way and a proof of its strong NP-hardness is provided. We also describe polynomial time algorithms for special cases of the problem.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2010, 20, 2; 385-390
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Building the library of RNA 3D nucleotide conformations using the clustering approach
    Autorzy:
    Zok, T.
    Antczak, M.
    Riedel, M.
    Nebel, D.
    Villmann, T.
    Lukasiak, P.
    Blazewicz, J.
    Szachniuk, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/329744.pdf
    Data publikacji:
    2015
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    RNA nucleotides
    conformer library
    torsion angles
    clustering
    neural gas
    Opis:
    An increasing number of known RNA 3D structures contributes to the recognition of various RNA families and identification of their features. These tasks are based on an analysis of RNA conformations conducted at different levels of detail. On the other hand, the knowledge of native nucleotide conformations is crucial for structure prediction and understanding of RNA folding. However, this knowledge is stored in structural databases in a rather distributed form. Therefore, only automated methods for sampling the space of RNA structures can reveal plausible conformational representatives useful for further analysis. Here, we present a machine learning-based approach to inspect the dataset of RNA three-dimensional structures and to create a library of nucleotide conformers. A median neural gas algorithm is applied to cluster nucleotide structures upon their trigonometric description. The clustering procedure is two-stage: (i) backbone- and (ii) ribose-driven. We show the resulting library that contains RNA nucleotide representatives over the entire data, and we evaluate its quality by computing normal distribution measures and average RMSD between data points as well as the prototype within each cluster.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2015, 25, 3; 689-700
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Exact and heuristic approaches to solve the Internet shopping optimization problem with delivery costs
    Autorzy:
    Lopez-Loces, M. C.
    Musial, J.
    Pecero, J. E.
    Fraire-Huacuja, H. J.
    Blazewicz, J.
    Bouvry, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/330508.pdf
    Data publikacji:
    2016
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    internet shopping optimization
    integer linear programming
    cellular processing algorithm
    heuristic algorithms
    optimization in e-commerce
    zakupy internetowe
    programowanie liniowe
    algorytm heurystyczny
    handel elektroniczny
    Opis:
    Internet shopping has been one of the most common online activities, carried out by millions of users every day. As the number of available offers grows, the difficulty in getting the best one among all the shops increases as well. In this paper we propose an integer linear programming (ILP) model and two heuristic solutions, the MinMin algorithm and the cellular processing algorithm, to tackle the Internet shopping optimization problem with delivery costs. The obtained results improve those achieved by the state-of-the-art heuristics, and for small real case scenarios ILP delivers exact solutions in a reasonable amount of time.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2016, 26, 2; 391-406
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-5 z 5

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