DNA Sequencing by Hybridization via Genetic Search

Authors:
Jacek Blazewicz;Ceyda Oguz;Aleksandra Swiercz;Jan Weglarz
Affiliations:
Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland, and the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 ...;Department of Industrial Engineering, Koç University, Istanbul, Turkey;Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland, and the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 ...;Institute of Computing Science, Poznań University of Technology, Piotrowo 2, 60-965 Poznań, Poland, and the Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 ...
Venue:
Operations Research
Year:
2006

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Abstract

An innovative approach to DNA sequencing by hybridization utilizes isothermic oligonucleotide libraries. In this paper, we demonstrate the utility of a genetic algorithm for the combinatorial portion of this new approach by incorporating characteristics of DNA sequencing by hybridization in addition to isothermic oligonucleotide libraries. Specialized crossover and mutation operators were developed for this purpose. After initial experiments for parameter adjustment, the performance of the genetic algorithm approach was evaluated with respect to previous methods in the literature. The results indicate that the proposed new approach is superior to previous approaches. The proposed new crossover operator that inherits some features of the structured weighted combinations might also be of value for some other combinatorial problems, including the traveling salesman problem.