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An algorithm for isothermic DNA sequencing

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Wybrane pełne teksty z tego czasopisma
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Języki publikacji
EN
Abstrakty
EN
In the paper, the problem of isothermic DNA sequencing by hybridization, without any errors in its input data, is presented and an exact polynomial-time algorithm solving the problem is described. The correctness of the algorithm is confirmed by an enumerative proof.
Twórcy
autor
  • Poznań University of Technology, Institute of Computing Science, 3 Piotrowo St., 60-965 Poznań, Poland
Bibliografia
  • [1] W. Bai ns and G. C. Smith, “A novel method for nuclei cacid sequence determination”, J. Theor. Biol. 135, 303–307 (1988).
  • [2] Yu. P. Lysov, V. L. Florentiev, A. A. Khorlin, K. R. Khrapko, V. V. Shik and A. D. Mirzabekov, “Determination of the nucleotide sequence of DNA using hybridization with oligonucleotides. A new method”, Dokl. Akad. Nauk SSSR 303, 1508–1511 (1988).
  • [3] E. M. Southern, United Kingdom Patent Application GB8810400 (1988).
  • [4] R. Drmanac, I. Labat, I. Brukner and R. Crkvenjakov, “Sequencing of megabase plus DNA by hybridization: theory of the method”, Genomics 4, 114–128 (1989).
  • [5] A. Apostolico and R. Giancarlo, “Sequence alignment in molecular biology”, in: Mathematical Support for Molecular Biology, ed.: M. Farach, F. Roberts, M. Waterman, Am. Math. Soc. DIMACS (1997).
  • [6] J. Błażewicz, P. Formanowicz, M. Kasprzak, W. T. Markiewicz and J. Węglarz, “DNA sequencing with positive and negative errors”, J. Comput. Biol. 6, 113–123 (1999).
  • [7] A. Guenoche, “Can we recover a sequence, just knowing all its subsequences of given length?”, CABIOS 8, 569–574 (1992).
  • [8] J. Setubal and J. Meidanis, Introduction to Computational Molecular Biology, Boston: PWS Publishing Company, (1997).
  • [9] M. S. Waterman, Introduction to Computational Biology. Maps, Sequences and Genomes, London: Chapman & Hall, (1995).
  • [10] P. A. Pevzner, “l-tuple DNA sequencing: computer analysis”, J. Biomol. Struct. Dyn. 7, 63–73 (1989).
  • [11] J. Błażewicz and M. Kasprzak, “Complexity of DNA sequencing by hybridization”, Theor. Comp. Sci. 290, 1459–1473 (2003).
  • [12] J. Błażewicz, P. Formanowicz, M. Kasprzak and W. T. Markiewicz, “Sequencing by hybridization with isothermic oligonucleotide libraries”, Disc. Applied Math., to be published.
  • [13] R. B. Wallace, M. J. Johnson, T. Hi orse, T. Mi ayke, E. H. Kawashima and K. Itakura, “The use of synthetic oligonucleotides as hybridization probes. Hybridization of oligonucleotides of mixed sequence to rabbit beta-globin DNA”, Nucl. Acids Res. 9, 879–894 (1981).
  • [14] J. Błażewicz, A. Hertz, D. Kobler and D. de Werra, “On some properties of DNA graphs”, Disc. Applied Math. 98, 1–19 (1999).
  • [15] J. Bang-Jensen and G. Gutin, Digraphs: Theory, Algorithms and Applications, Berlin: Springer-Verlag, 2001.
  • [16] E. Lawler, Combinatorial Optimization: Networks and Matroids, Holt, New York: Rinehart and Winston, 1976.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BPG5-0001-0012
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