Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments

Zhixiang Chen, Bin Fu, Robert Schweller, Boting Yang, Zhiyu Zhao, Binhai Zhu

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

In this paper, we develop a probabilistic model to approach two scenarios in reality about the singular haplotype reconstruction problem - the incompleteness and inconsistency occurred in the DNA sequencing process to generate the input haplotype fragments and the common practice used to generate synthetic data in experimental algorithm studies. We design three algorithms in the model that can reconstruct the two unknown haplotypes from the given matrix of haplotype fragments with provable high probability and in time linear in the size of the input matrix. We also present experimental results that conform with the theoretical efficient performance of those algorithms. The software of our algorithms is available for public access and for real-time on-line demonstration.

Original languageEnglish (US)
Title of host publicationSeries on Advances in Bioinformatics and Computational Biology
Pages333-342
Number of pages10
Volume6
StatePublished - 2008
Event6th Asia-Pacific Bioinformatics Conference, APBC 2008 - Kyoto, Japan
Duration: Jan 14 2008Jan 17 2008

Other

Other6th Asia-Pacific Bioinformatics Conference, APBC 2008
CountryJapan
CityKyoto
Period1/14/081/17/08

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Demonstrations
Statistical Models

Keywords

  • Haplotype reconstruction
  • Incompleteness errors
  • Inconsis- tency errors
  • Probabilistic algorithms
  • SNP fragments

ASJC Scopus subject areas

  • Bioengineering
  • Information Systems

Cite this

Chen, Z., Fu, B., Schweller, R., Yang, B., Zhao, Z., & Zhu, B. (2008). Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments. In Series on Advances in Bioinformatics and Computational Biology (Vol. 6, pp. 333-342)

Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments. / Chen, Zhixiang; Fu, Bin; Schweller, Robert; Yang, Boting; Zhao, Zhiyu; Zhu, Binhai.

Series on Advances in Bioinformatics and Computational Biology. Vol. 6 2008. p. 333-342.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chen, Z, Fu, B, Schweller, R, Yang, B, Zhao, Z & Zhu, B 2008, Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments. in Series on Advances in Bioinformatics and Computational Biology. vol. 6, pp. 333-342, 6th Asia-Pacific Bioinformatics Conference, APBC 2008, Kyoto, Japan, 1/14/08.
Chen Z, Fu B, Schweller R, Yang B, Zhao Z, Zhu B. Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments. In Series on Advances in Bioinformatics and Computational Biology. Vol. 6. 2008. p. 333-342
Chen, Zhixiang ; Fu, Bin ; Schweller, Robert ; Yang, Boting ; Zhao, Zhiyu ; Zhu, Binhai. / Linear time probabilistic algorithms for the singular haplotype reconstruction problem from SNP fragments. Series on Advances in Bioinformatics and Computational Biology. Vol. 6 2008. pp. 333-342
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