16. Phasing Genotypes Using a Hidden Markov Model

  1. Ion I. Mǎndoiu2 and
  2. Alexander Zelikovsky3
  1. P. Rastas,
  2. M. Koivisto,
  3. H. Mannila and
  4. E. Ukkonen

Published Online: 9 AUG 2007

DOI: 10.1002/9780470253441.ch16

Bioinformatics Algorithms: Techniques and Applications

Bioinformatics Algorithms: Techniques and Applications

How to Cite

Rastas, P., Koivisto, M., Mannila, H. and Ukkonen, E. (2008) Phasing Genotypes Using a Hidden Markov Model, in Bioinformatics Algorithms: Techniques and Applications (eds I. I. Mǎndoiu and A. Zelikovsky), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470253441.ch16

Editor Information

  1. 2

    Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, USA

  2. 3

    Department of Computer Science, Georgia State University, Atlanta, GA, USA

Author Information

  1. Department of Computer Science and HIIT Basic Research Unit, University of Helsinki, Finland

Publication History

  1. Published Online: 9 AUG 2007
  2. Published Print: 8 FEB 2008

ISBN Information

Print ISBN: 9780470097731

Online ISBN: 9780470253441

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Keywords:

  • partition ligation (PL) technique;
  • expectation-maximization (EM) algorithms;
  • Initialization and Model Training

Summary

This chapter contains sections titled:

  • Introduction

  • A Hidden Markov Model for Recombinant Haplotypes

  • Learning the HMM from Unphased Genotype Data

  • Haplotype Reconstruction

  • Experimental Results

  • Discussion

  • Acknowledgments

  • References