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Abstrakty
Sequencing by hybridization (SBH) is a method of reading DNA sequence from its smaller fragments. Such a method has been proposed in late 1980s and until the emergence of the new generation sequencing it has been widely used and improved. Since the initial, classical approach to SBH, many modifications and enhancements was proposed, aimed at improving the preciseness and the length of sequences which can be unambiguously read. Even now, for some DNA sequences sequencing by hybridization can still be used effectively and at a low cost. In this paper many different approaches to the SBH will be described, mainly from the points of view of algorithms and computational complexity.
Słowa kluczowe
Rocznik
Tom
Strony
259--271
Opis fizyczny
Bibliogr. 51 poz., tab.
Twórcy
autor
- Institute of Computing Science Poznan University of Technology
autor
- Institute of Computing Science Poznan University of Technology
- Institute of Bioorganic Chemistry Polish Academy of Sciences
autor
- Institute of Computing Science Poznan University of Technology
- Institute of Bioorganic Chemistry Polish Academy of Sciences
Bibliografia
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- [29] K. Kwarciak, M. Radom, P. Formanowicz, A multilevel ant colony optimization algorithm for DNA sequencing by hybridization with multiplicity information available. in press, 2015.
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- [41] M. Radom and P. Formanowicz, Algorithms for sequencing by hybridization problems based on non-classical DNA chips, Przeglad Elektrotechniczny 10, 97–100 (2010).
- [42] M.RadomandP.Formanowicz,Analgorithmforsequencing by hybridization based on an alternating DNA chip, Computational Biology and Chemistry 10(3), 67–78 (2018).
- [43] P. Zhang, M. Egholm, N. Paul, M. Pingle, D. Bergstrom, Peptide nucleic acid-DNA duplexes containing the universal base 3-nitropyrrole, Methods 23, 132–140 (2001).
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- [45] A. Frieze, F. Preparata, E. Upfal, Optimal reconstruction of a sequence from its probes, Journal of Computational Biology 6, 361–368 (1999).
- [46] F. Preperata and J. Oliver, DNA sequencing by hybridization using semi-degeneratae bases, Journal of Computational Biology 11, 753–765 (2004).
- [47] P. Sachadyn and J. Kur, Reducing the number of microlocations in oligonucleotide microchip matrices by the application of degenerate oligonucleotides, Journal of Computational Biology 197, 393–401 (1999).
- [48] J. Błażewicz, P. Formanowicz, M. Kasprzak, W. Markiewicz,Sequencing by hybridization with isothermic oligonucleotide libraries, Discrete Applied Mathematics 145, 40–51 (2004).
- [49] J. Błażewicz and M. Kasprzak, Computational complexity of isothermic DNA sequencing by hybridization, Discrete Applied Mathematics 154, 718–729 (2006).
- [50] J. Błażewicz, P. Formanowicz, M. Kasprzak, W. Markiewicz,A. Świercz, Tabu search algorithm for DNA sequencing by hybridization with isothermic libraries, Computational Biology and Chemistry 28, 11–19 (2004).
- [51] J. Błażewicz, P. Formanowicz, Multistage isothermic sequencing by hybridization, Computational Biology and Chemistry 29, 69–77 (2005).
Uwagi
Opracowanie rekordu w ramach umowy 509/P-DUN/2018 ze środków MNiSW przeznaczonych na działalność upowszechniającą naukę (2018).
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-318feb4b-3aad-4d80-8e13-a90ca75f96fc