Mapping DNA by stochastic relaxation
Advances in Applied Mathematics
Multiple solutions of DNA restriction mapping problems
Advances in Applied Mathematics
Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
The Enhanced Double Digest Problem for DNA Physical Mapping
SWAT '00 Proceedings of the 7th Scandinavian Workshop on Algorithm Theory
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The strongly NP-complete Double Digest Problem (DDP) for physical mapping of DNA, is now used for efficient genotyping. An instance of DDP has multiple distinct solutions. Existing methods produce a single solution, and are slow for large instances. We employ a type of equivalence among the distinct solutions to obtain almost all of them. Our method comprises of first finding a solution from each equivalence class by an elitist genetic algorithm, and then generating entire classes. Notable efficiency was achieved due to significant reduction in search space.