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Pacific-Asia Conference on Knowledge Discovery and Data Mining

PAKDD 2009: Advances in Knowledge Discovery and Data Mining pp 647–655Cite as

Computing Substitution Matrices for Genomic Comparative Analysis

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Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 5476))

Abstract

Substitution matrices describe the rates of mutating one character in a biological sequence to another character, and are important for many knowledge discovery tasks such as phylogenetic analysis and sequence alignment. Computing substitution matrices for very long genomic sequences of divergent or even unrelated species requires sensitive algorithms that can take into account differences in composition of the sequences. We present a novel algorithm that addresses this by computing a nucleotide substitution matrix specifically for the two genomes being aligned. The method is founded on information theory and in the expectation maximisation framework. The algorithm iteratively uses compression to align the sequences and estimates the matrix from the alignment, and then applies the matrix to find a better alignment until convergence. Our method reconstructs, with high accuracy, the substitution matrix for synthesised data generated from a known matrix with introduced noise. The model is then successfully applied to real data for various malaria parasite genomes, which have differing phylogenetic distances and composition that lessens the effectiveness of standard statistical analysis techniques.

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Author information

Authors and Affiliations

  1. Clayton School of Information Technology, Monash University, Clayton, 3800, Australia

    Minh Duc Cao, Trevor I. Dix & Lloyd Allison

  2. Faculty of Information & Communication Technologies, Swinburne University of Technology, Hawthorn, 3122, Australia

    Trevor I. Dix

Authors
  1. Minh Duc Cao
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  2. Trevor I. Dix
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  3. Lloyd Allison
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Editor information

Editors and Affiliations

  1. Sirindhorn International Institute of Technology, Thammasat University, 131 Moo 5 Tiwanont Road, 12000, Bangkadi, Muang, Pathumthani, Thailand

    Thanaruk Theeramunkong

  2. Dept. of Computer Engineering, Faculty of Engineering, Chulalongkorn University, 10330, Bangkok, Thailand

    Boonserm Kijsirikul

  3. Faculty of Science & Engineering, York University, 355 Lumbers Building, 4700 Keele Street, M3J 1P3, Toronto, Ontario, Canada

    Nick Cercone

  4. School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, 923-1292, Ishikawa, Japan

    Tu-Bao Ho

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© 2009 Springer-Verlag Berlin Heidelberg

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Cao, M.D., Dix, T.I., Allison, L. (2009). Computing Substitution Matrices for Genomic Comparative Analysis. In: Theeramunkong, T., Kijsirikul, B., Cercone, N., Ho, TB. (eds) Advances in Knowledge Discovery and Data Mining. PAKDD 2009. Lecture Notes in Computer Science(), vol 5476. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-01307-2_64

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  • DOI: https://doi.org/10.1007/978-3-642-01307-2_64

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-01306-5

  • Online ISBN: 978-3-642-01307-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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