Abstract
In the paper, a new hybrid genetic algorithm solving the DNA sequencing problem with negative and positive errors is presented. The algorithm has as its input a set of oligonucleotides coming from a hybridization experiment. The aim is to reconstruct an original DNA sequence of a known length on the basis of this set. No additional information about the oligonucleotides nor about the errors is assumed. Despite that, the algorithm returns for computationally hard instances surprisingly good results, of a very high similarity to original sequences.
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References
Bains, W. and G.C. Smith. (1988). “A Novel Method for Nucleic Acid Sequence Determination.” Journal of Theoretical Biology 135, 303–307.
Błażewicz, J., J. Kaczmarek, M. Kasprzak, W.T. Markiewicz, and J. Węglarz. (1997). “Sequential and Parallel Algorithms for DNA Sequencing.” Computer Applications in the Biosciences 13, 151–158.
Błażewicz, J., P. Formanowicz, M. Kasprzak, W.T. Markiewicz, and J. Węglarz. (1999a). “DNA Sequencing with Positive and Negative Errors.” Journal of Computational Biology 6, 113–123.
Błażewicz, J., P. Formanowicz, F. Glover, M. Kasprzak, and J. Węglarz. (1999b). “An Improved Tabu Search Algorithm for DNA Sequencing with Errors.” In Proceedings of the III Metaheuristics International Conference MIC'99, pp. 69–75.
Błażewicz, J., P. Formanowicz, M. Kasprzak, W.T. Markiewicz, and J. Węglarz. (2000). “Tabu Search for DNA Sequencing with False Negatives and False Positives.” European Journal of Operational Research 125, 257–265.
Błażewicz, J. and M. Kasprzak. (2002). “Complexity of DNA Sequencing by Hybridization.” Theoretical Computer Science, to appear.
Caviani Pease, A., D. Solas, E.J. Sullivan, M.T. Cronin, C.P. Holmes, and S.P.A. Fodor. (1994). “Light-Generated Oligonucleotide Arrays for Rapid DNA Sequence Analysis.” In Proceedings of the National Academy of Sciences of the USA 91, pp. 5022–5026.
Drmanac, R., I. Labat, I. Brukner, and R. Crkvenjakov. (1989). “Sequencing of Megabase Plus DNA by Hybridization: Theory of the Method.” Genomics 4, 114–128.
Drmanac, R., I. Labat, and R. Crkvenjakov. (1991). “An Algorithm for the DNA Sequence Generation from k-tupleWord Contents of the Minimal Number of Random Fragments.” Journal of Biomolecular Structure and Dynamics 8, 1085–1102.
Fodor, S.P.A., J.L. Read, M.C. Pirrung, L. Stryer, A.T. Lu, and D. Solas. (1991). “Light-Directed, Spatially Addressable Parallel Chemical Synthesis.” Science 251, 767–773.
Glover, F. (1977). “Heuristics for Integer Programming Using Surrogate Constraints.” Decision Sciences 8, 156–166.
Glover, F. and M. Laguna. (1977). Tabu Search. Norwell: Kluwer Academic Publishers.
Goldberg, D.E. (1989). Genetic Algorithms in Search, Optimization, and Machine Learning. Reading: Addison-Wesley.
Grefenstette, J.J., R. Gopal, B.J. Rosmaita, and D. Van Gucht. (1985). “Genetic Algorithms for the Traveling Salesman Problem.” In Proceedings of International Conference on Genetic Algorithms and Their Applications, pp. 160–168.
Hagstrom, J.N., R. Hagstrom, R. Overbeek, M. Price, and L. Schrage. (1994). “Maximum Likelihood Genetic Sequence Reconstruction from Oligo Content.” Networks 24, 297–302.
Holland, J.H. (1975). Adaptation in Natural and Artificial Systems. Ann Arbor: University of Michigan Press.
Lipshutz, R.J. (1993). “Likelihood DNA Sequencing by Hybridization.” Journal of Biomolecular Structure and Dynamics 11, 637–653.
Lysov, Yu. P., V.L. Florentiev, A.A. Khorlin, K.R. Khrapko, V.V. Shik, and A.D. Mirzabekov. (1988). “Determination of the Nucleotide Sequence of DNA Using Hybridization with Oligonucleotides. A New Method.” Doklady Akademii Nauk SSSR 303, 1508–1511.
Markiewicz, W.T., K. Andrych-Rożek, M. Markiewicz, A. Żebrowska, and A. Astriab. (1994). “Synthesis of Oligonucleotides Permanently Linked with Solid Supports for Use as Synthetic Oligonucleotide Combinatorial Libraries. Innovations in Solid Phase Synthesis.” In R. Epton (ed.), Biological and Biomedical Applications. Birmingham: Mayflower Worldwide, pp. 339–346.
Pevzner, P.A. (1989). “l-tuple DNA Sequencing: Computer Analysis.” Journal of Biomolecular Structure and Dynamics 7, 63–73.
Southern, E.M. (1988). United Kingdom Patent Application GB8810400.
Waterman, M.S. (1995). Introduction to Computational Biology. Maps, Sequences and Genomes. London: Chapman &; Hall.
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Błażewicz, J., Kasprzak, M. & Kuroczycki, W. Hybrid Genetic Algorithm for DNA Sequencing with Errors. Journal of Heuristics 8, 495–502 (2002). https://doi.org/10.1023/A:1016589707123
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DOI: https://doi.org/10.1023/A:1016589707123