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A Faster Haplotyping Algorithm Based on Block Partition, and Greedy Ligation Strategy

  • Xiaohui Yao
  • Yun Xu
  • Jiaoyun Yang
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6840)

Abstract

Haplotype played a very important role in the study of some disease gene and drug response tests over the past years. However, it is both time consuming and very costly to obtain haplotypes by experimental way. Therefore haplotype inference was proposed which deduce haplotypes from the genotypes through computing methods. Some genetic models were presented to solve the haplotype inference problem, and Maximum Parsimony model was one of them, but at present the methods based on this principle are either simple greedy heuristic or exact ones, which are adequate only for moderate size instances. In this paper, we presented a faster greedy algorithm named FHBPGL applying partition and ligation strategy. Theoretical analysis shows that this strategy can reduce the running time for large scale dataset and following experiments demonstrated that our algorithm gained comparable accuracy compared to exact haplotyping algorithms with less time.

Keywords

Maximum Parsimony Heterozygous Locus Haplotype Inference Block Partition Perfect Phylogeny 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Xiaohui Yao
    • 1
    • 2
  • Yun Xu
    • 1
    • 2
  • Jiaoyun Yang
    • 1
    • 2
  1. 1.Department of Computer ScienceUniversity of Science and Technology of ChinaHefeiChina
  2. 2.Anhui Province-MOST Co-Key Laboratory of High Performance Computing and Its ApplicationUniversity of Science and Technology of ChinaHefeiChina

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