Abstract
We describe a multistart heuristic using an adaptive memory strategy for the problem of sequencing by hybridization. The memory-based strategy is able to significantly improve the performance of memoryless construction procedures, in terms of solution quality and processing time. Computational results show that the new heuristic obtains systematically better solutions than more involving and time consuming techniques such as tabu search and genetic algorithms.
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References
Aiex, R.M., Resende, M.G.C., Ribeiro, C.C.: Probability distribution of solution time in GRASP: An experimental investigation. Journal of Heuristics 8, 343–373 (2002)
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Wheeler, D.L.: Genbank: Update. Nucleic Acids Research 32, D23–D26 (2004)
Blazewicz, J., Formanowicz, P., Guinand, F., Kasprzak, M.: A heuristic managing errors for DNA sequencing. Bioinformatics 18, 652–660 (2002)
Blazewicz, J., Formanowicz, P., Kasprzak, M., Markiewicz, W.T., Weglarz, T.: Tabu search for DNA sequencing with false negatives and false positives. European Journal of Operational Research 125, 257–265 (2000)
Blazewicz, J., Kasprzak, M.: Complexity of DNA sequencing by hybridization. Theoretical Computer Science 290, 1459–1473 (2003)
Endo, T.A.: Probabilistic nucleotide assembling method for sequencing by hybridization. Bioinformatics 20, 2181–2188 (2004)
Fleurent, C., Glover, F.: Improved constructive multistart strategies for the quadratic assignment problem using adaptive memory. INFORMS Journal on Computing 11, 198–204 (1999)
Pevzner, P.A.: Computational molecular biology: An algorithmic approach. MIT Press, Cambridge (2000)
Waterman, M.S.: Introduction to computational biology: Maps, sequences and genomes. Chapman & Hall, Boca Raton (1995)
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© 2005 Springer-Verlag Berlin Heidelberg
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Fernandes, E.R., Ribeiro, C.C. (2005). Using an Adaptive Memory Strategy to Improve a Multistart Heuristic for Sequencing by Hybridization. In: Nikoletseas, S.E. (eds) Experimental and Efficient Algorithms. WEA 2005. Lecture Notes in Computer Science, vol 3503. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11427186_2
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DOI: https://doi.org/10.1007/11427186_2
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-25920-6
Online ISBN: 978-3-540-32078-4
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