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Haplotyping a Diploid Single Individual with a Fast and Accurate Enumeration Algorithm

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Intelligent Computing Theories and Application (ICIC 2016)

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Abstract

The minimum error correction (MEC) model is one of the important computational models for determining haplotype information from sequencing data, i.e., single individual single nucleotide polymorphism (SNP) haplotyping, haplotype reconstruction or haplotype assembly. Due to the NP-hardness of the model, a fast and accurate enumeration algorithm is proposed for solving it. The presented algorithm reconstructs the SNP sites of a pair of haplotypes one after another. It enumerates two kinds of SNP values, i.e., (0 1)T and (1 0)T, for the SNP site being reconstructed, and chooses the one with more support coming from the SNP fragments that are covering the corresponding SNP site. The experimental comparisons were conducted among the presented algorithm, the FAHR, the Fast Hare and the DGS algorithms. The results prove that our algorithm can get higher reconstruction rate than the other three algorithms.

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Notes

  1. 1.

    Download from http://hapmap.ncbi.nlm.nih.gov/downloads/phasing/2007-08_rel22/phased/.

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Acknowledgments

The authors are grateful to anonymous referees for their helpful comments. This research is supported by the National Natural Science Foundation of China under Grant No.61363035 and No.61502111, Guangxi Natural Science Foundation under Grant No. 2015GXNSFAA139288, No. 2013GXNSFBA019263 and No. 2012GXNSFAA053219, Research Fund of Guangxi Key Lab of Multisource Information Mining & Security No. 14-A-03-02 and No. 15-A-03-02, “Bagui Scholar” Project Special Funds, Guangxi Collaborative Innovation Center of Multi-source Information Integration and Intelligent Processing.

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Correspondence to Jingli Wu .

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Chen, X., Wu, J., Li, L. (2016). Haplotyping a Diploid Single Individual with a Fast and Accurate Enumeration Algorithm. In: Huang, DS., Bevilacqua, V., Premaratne, P. (eds) Intelligent Computing Theories and Application. ICIC 2016. Lecture Notes in Computer Science(), vol 9771. Springer, Cham. https://doi.org/10.1007/978-3-319-42291-6_40

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  • DOI: https://doi.org/10.1007/978-3-319-42291-6_40

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