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An Enhanced Genetic Algorithm for DNA Sequencing by Hybridization with Positive and Negative Errors
Thang N. Bui and Waleed A. Youssef
Department of Computer Science, The Pennsylvania State University at Harrisburg, Middletown, PA 17057tbui@psu.edu
wuy101@psu.edu
Abstract. This paper describes a genetic algorithm for the DNA sequencing problem. The algorithm allows the input spectrum to contain both positive and negative errors as could be expected from a hybridization experiment. The main features of the algorithm include a preprocessing step that reduces the size of the input spectrum and an efficient local optimization. In experimental tests, the algorithm performed very well against existing algorithms. The algorithm also performed very well on a large data set generated in this paper from real genomes data.
LNCS 3103, p. 908 ff.
lncs@springer.de
© Springer-Verlag Berlin Heidelberg 2004