Abstract
In this paper we propose and study the behavior of a new heuristic algorithm for the DNA fragment assembly problem: PALS. The DNA fragment assembly is a problem to be solved in the early phases of the genome project and thus is very important since the other steps depend on its accuracy. This is an NP-hard combinatorial optimization problem which is growing in importance and complexity as more research centers become involved on sequencing new genomes. Various heuristics, including genetic algorithms, have been designed for solving the fragment assembly problem, but since this problem is a crucial part of any sequencing project, better assemblers are needed. Our proposal is a very efficient assembler that allows to find optimal solutions for large instances of this problem, considerably faster than its competitors and with high accuracy.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Setubal, J., Meidanis, J.: Introduction to Computational Molecular Biology, chapter 4 - Fragment Assembly of DNA, pp. 105–139. University of Campinas, Brazil (1997)
Green, P.: Phrap. http://www.mbt.washington.edu/phrap.docs/phrap.html
Sutton, G.G., White, O., Adams, M.D., Kerlavage, A.R.: TIGR Assembler: A new tool for assembling large shotgun sequencing projects. In: Genome Science & Technology, pp. 9–19 (1995)
Chen, T., Skiena, S.S.: Trie-based data structures for sequence assembly. In: The Eighth Symposium on Combinatorial Pattern Matching, pp. 206–223 (1998)
Huang, X., Madan, A.: CAP3: A DNA sequence assembly program. Genome Research 9, 868–877 (1999)
Myers, E.W.: Towards simplifying and accurately formulating fragment assembly. Journal of Computational Biology 2(2), 275–290 (2000)
Pevzner, P.A.: Computational molecular biology: An algorithmic approach. MIT Press, London (2000)
Luque, G., Alba, E.: Metaheuristics for the DNA Fragment Assembly Problem. International Journal of Computational Intelligence Research 1(2), 98–108 (January 2006)
Parsons, R., Forrest, S., Burks, C.: Genetic algorithms, operators, and DNA fragment assembly. Machine Learning 21, 11–33 (1995)
Li, L., Khuri, S.: A comparison of DNA fragment assembly algorithms. In: International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, pp. 329–335 (2004)
Lin, S., Kernighan, B.W.: An effective heuristic algorithm for TSP. Operations Research 21, 498–516 (1973)
Engle, M.L., Burks, C.: Artificially generated data sets for testing DNA fragment assembly algorithms. Genomics 16 (1993)
Jing, Y., Khuri, S.: Exact and heuristic algorithms for the DNA fragment assembly problem. In: Proceedings of the IEEE Computer Society Bioinformatics Conference, pp. 581–582. IEEE Press, New York (2003)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Alba, E., Luque, G. (2007). A New Local Search Algorithm for the DNA Fragment Assembly Problem. In: Cotta, C., van Hemert, J. (eds) Evolutionary Computation in Combinatorial Optimization. EvoCOP 2007. Lecture Notes in Computer Science, vol 4446. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71615-0_1
Download citation
DOI: https://doi.org/10.1007/978-3-540-71615-0_1
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-71614-3
Online ISBN: 978-3-540-71615-0
eBook Packages: Computer ScienceComputer Science (R0)