Self-organizing map approaches for the haplotype assembly problem

Ling-Yun Wu, Zhenping Li, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen

Mathematics and Computers in Simulation (MATCOM), 2009, vol. 79, issue 10, 3026-3037

Abstract: Haplotype assembly is to reconstruct a pair of haplotypes from SNP values observed in a set of individual DNA fragments. In this paper, we focus on studying minimum error correction (MEC) model for the haplotype assembly problem and explore self-organizing map (SOM) methods for this problem. Specifically, haplotype assembly by MEC is formulated into an integer linear programming model. Since the MEC problem is NP-hard and thus cannot be solved exactly within acceptable running time for large-scale instances, we investigate the ability of classical SOMs to solve the haplotype assembly problem with MEC model. Then, aiming to overcome the limits of classical SOMs, a novel SOM approach is proposed for the problem. Extensive computational experiments on both synthesized and real datasets show that the new SOM-based algorithm can efficiently reconstruct haplotype pairs in a very high accuracy under realistic parameter settings. Comparison with previous methods also confirms the superior performance of the new SOM approach.

Keywords: SNP; Haplotype assembly; Minimum error correction; Self-organizing map; Neural network (search for similar items in EconPapers)
Date: 2009
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Citations: View citations in EconPapers (1)

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Persistent link: https://EconPapers.repec.org/RePEc:eee:matcom:v:79:y:2009:i:10:p:3026-3037

DOI: 10.1016/j.matcom.2009.01.021

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