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International Conference on Intelligent Computing

ICIC 2011: Bio-Inspired Computing and Applications pp 537–544Cite as

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

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Part of the book series: Lecture Notes in Computer Science ((LNBI,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.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Science and Technology of China, Hefei, Anhui, 230026, China

    Xiaohui Yao, Yun Xu & Jiaoyun Yang

  2. Anhui Province-MOST Co-Key Laboratory of High Performance Computing and Its Application, University of Science and Technology of China, Hefei, Anhui, 230027, China

    Xiaohui Yao, Yun Xu & Jiaoyun Yang

Authors
  1. Xiaohui Yao
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  2. Yun Xu
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  3. Jiaoyun Yang
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Editor information

Editors and Affiliations

  1. School of Electronics and Information Engineering, Tongji University, 4800 Caoan Road, 201804, Shanghai, China

    De-Shuang Huang

  2. School of Computer and Communication Engineering, Zhengzhou University of Light Industry, No. 5, Dongfeng Road, Jinshui District, 450002, Zhengzhou, Henan, China

    Yong Gan

  3. School of Electrical, Computer & Telecommunications Engineering, University of Wollongong, 2522, P.O. Box, North Wollongong, NSW, Australia

    Prashan Premaratne

  4. School of Computer Science and Engineering, Inha University, 402-751, Inchon, Korea

    Kyungsook Han

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© 2012 Springer-Verlag Berlin Heidelberg

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Yao, X., Xu, Y., Yang, J. (2012). A Faster Haplotyping Algorithm Based on Block Partition, and Greedy Ligation Strategy. In: Huang, DS., Gan, Y., Premaratne, P., Han, K. (eds) Bio-Inspired Computing and Applications. ICIC 2011. Lecture Notes in Computer Science(), vol 6840. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-24553-4_71

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  • DOI: https://doi.org/10.1007/978-3-642-24553-4_71

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-24552-7

  • Online ISBN: 978-3-642-24553-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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