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Bioinformatics Advance Access published online on February 24, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti352
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 23, 2004
Revised January 31, 2005
Accepted February 22, 2005

Article

Haplotype reconstruction from SNP fragments by Minimum Error Correction

Rui-Sheng Wang 1*, Ling-Yun Wu 1, Zhen-Ping Li 2, and Xiang-Sun Zhang 1

1 Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100080, China
2 Beijing Materials Institute, Beijing 101149, China

* To whom correspondence should be addressed.
Rui-Sheng Wang, E-mail: wangrsh{at}amss.ac.cn


  Abstract

Motivation: Haplotype reconstruction based on aligned SNP fragments is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. An important computational model of this problem is the Minimum Error Correction (MEC) model, which has been suggested in several literatures. The model retrieves a pair of haplotypes by correcting minimum number of SNPs in given genome fragments coming from an individual's DNA.

Results: In the first part of this paper, an exact algorithm for the MEC model is presented. Due to the NP-hardness of the MEC model, we also design a heuristic method based on genetic algorithm (GA). The designed GA is intended to solve large size problems and has very good performance. The strength and weakness of the MEC model are shown through experimental results on real data and simulation data. In the second part of this paper, to overcome the weakness of the MEC model, a new computational model is proposed, which simultaneously employs genotype information of an individual in the process of SNP correction, then is called MEC with genotype information (shortly, MEC/GI). Computational results on extensive data sets show the new model has much higher accuracy of haplotype reconstruction than the pure MEC model.


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