Iterated Local Search for de Novo Genomic Sequencing
The sequencing process of a DNA chain for reading its components supposes a complex process, since only small DNA fragments can be read nowadays. Therefore, the use of optimization algorithms is required to rebuild a single chain from all the small pieces. We address here a simplified version of the problem, in which no errors in the sequencing process are allowed. The methods typically used in the literature for this problem are not satisfactory when solving realistic size instances, so there is a need for new more efficient and accurate methods. We propose a new iterated local search algorithm, highly competitive with the best algorithms in the literature, and considerably faster.
KeywordsPerturbation Method Small Instance Iterate Local Search Large Problem Instance Swap Operation
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- 1.Alba, E., Dorronsoro, B.: Cellular Genetic Algorithms. In: Operations Research/Compuer Science Interfaces. Springer, Heidelberg (2008)Google Scholar
- 5.Dorronsoro, B.: The jcell framework (2007), http://neo.lcc.uma.es/Software/JCell/
- 6.Dorronsoro, B., Alba, E., Luque, G., Bouvry, P.: A Self-Adaptive Cellular Memetic Algorithm for the DNA Fragment Assembly Problem. In: Proc. of the IEEE Congress on Evolutionary Computation (CEC), pp. 2656–2663 (2008)Google Scholar
- 8.Kikuchi, S., Chakraborty, G.: Heuristically tuned GA to solve genome fragment assembly problem. In: IEEE CEC 2006, pp. 1491–1498 (2006)Google Scholar
- 9.Kim, S.: A structured Pattern Matching Approach to Shotgun Sequence Assembly. PhD thesis, Computer Science Department, The University of Iowa (1997)Google Scholar
- 10.Li, L., Khuri, S.: A Comparison of DNA Fragment Assembly Algorithms. In: Int. Conf. METMBS, pp. 329–335 (2004)Google Scholar
- 11.Parsons, R., Forrest, S., Burks, C.: Genetic algorithms, operators and DNA fragment assembly. Machine Learning 21, 11–33 (1995)Google Scholar
- 12.Pop, M.: Shotgun sequence assembly. Advances in Computers 60, 194–248 (2004)Google Scholar
- 13.Setubal, J., Meidanis, J.: Introduction to Computational Molecular Biology. Fragment Assembly of DNA, ch. 4, pp. 105–139. University of Campinas, Brazil (1997)Google Scholar