Genetic Algorithms in Search, Optimization and Machine Learning
Genetic Algorithms in Search, Optimization and Machine Learning
WABI '02 Proceedings of the Second International Workshop on Algorithms in Bioinformatics
Opportunities for Combinatorial Optimization in Computational Biology
INFORMS Journal on Computing
Computational Biology and Chemistry
Haplotype assembly from aligned weighted SNP fragments
Computational Biology and Chemistry
On the complexity of several haplotyping problems
WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics
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The algorithms that are based on the Weighted Minimum Letter Flips (WMLF) model are more accurate in haplotype reconstruction than those based on the Minimum Letter Flips (MLF) model, but WMLF is effective only when the error rate in SNP fragments is low. In this paper, we first establish a new computational model that employs the related genotype information as an improvement of the WMLF model and show its NP-hardness, and then we propose an efficient genetic algorithm to solve for the haplotype assembly problem. The results of experiments on a real data set indicate that the introduction of genotype information to the WMLF model is quite effective in improving the reconstruction rate especially when the error rate in SNP fragments is high.