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 Scopus citations

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 publicationProceedings of 6th Asia-Pacific Bioinformatics Conference, APBC 2008
Pages333-342
Number of pages10
StatePublished - Dec 1 2008
Event6th Asia-Pacific Bioinformatics Conference, APBC 2008 - Kyoto, Japan
Duration: Jan 14 2008Jan 17 2008

Publication series

NameSeries on Advances in Bioinformatics and Computational Biology
Volume6
ISSN (Print)1751-6404

Other

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

Keywords

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

ASJC Scopus subject areas

  • Bioengineering
  • Information Systems

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  • 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 Proceedings of 6th Asia-Pacific Bioinformatics Conference, APBC 2008 (pp. 333-342). (Series on Advances in Bioinformatics and Computational Biology; Vol. 6).