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Haplotyping a single triploid individual based on genetic algorithm

Issue title: Frontiers in Biomedical Engineering and Biotechnology – Proceedings of the 3rd International Conference on Biomedical Engineering and Biotechnology, 25–28 September 2014, Beijing, China

Article type: Research Article

Authors: Wu, Jingli; | Chen, Xixi | Li, Xianchen

Affiliations: Department of Computer Science, Guangxi Normal University, Guilin 541004, China

Note: [] Corresponding author: Jingli Wu, Department of Computer Science, Guangxi Normal University, Guilin 541004, China. Tel.: +86 13617832552; Fax: +86-773-5811621; E-mail: [email protected].

Keywords: Triploid, haplotype, Single nucleotide polymorphism (SNP), the minimum error correction, genetic algorithm

DOI: 10.3233/BME-141204

Journal: Bio-Medical Materials and Engineering, vol. 24, no. 6, pp. 3753-3762, 2014

Published: 2014
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Abstract

The minimum error correction model is an important combinatorial model for haplotyping a single individual. In this article, triploid individual haplotype reconstruction problem is studied by using the model. A genetic algorithm based method GTIHR is presented for reconstructing the triploid individual haplotype. A novel coding method and an effectual hill-climbing operator are introduced for the GTIHR algorithm. This relatively short chromosome code can lead to a smaller solution space, which plays a positive role in speeding up the convergence process. The hill-climbing operator ensures algorithm GTIHR converge at a good solution quickly, and prevents premature convergence simultaneously. The experimental results prove that algorithm GTIHR can be implemented efficiently, and can get higher reconstruction rate than previous algorithms.

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