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Discovering Patterns in Gene Order

  • Laxmi ParidaEmail author
  • Niina Haiminen
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 855)

Abstract

Various genetic events during the process of natural evolution shape the landscape of the genomes. In this chapter, we explore an approach to investigating multiple genomes in order to unravel their complex relationships that go beyond their placement on a phylogeny. To this end, we treat genes as the smallest syntactic unit on the genome and explore their relative organization across multiple genomes. In the first half of the chapter, we discuss mathematical models to capture the combinatorial structures of this relative organization and statistical models to study their distributions. In the second half of the chapter, we apply these models to analyze the relationship between three closely related plant genomes.

Key words

Gene cluster Gene order comparison Pattern significance Permutation pattern Whole genome analysis Pattern discovery Statistical significance Maximal PQ trees Plant gene order 

Notes

Acknowledgments

We would like to thank Alex Feltus for providing the genomic characteristics for the three plant species (Fig. 3).

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.IBM Thomas J. Watson Research CenterYorktown HeightsUSA

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