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Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution

  • Qian Zhu
  • Zaky Adam
  • Vicky Choi
  • David Sankoff
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4983)

Abstract

We present a parametrized definition of gene clusters that allows us to control the emphasis placed on conserved order within a cluster. Though motivated by biological rather than mathematical considerations, this parameter turns out to be closely related to the maximum bandwidth parameter of a graph. Our focus will be on how this parameter affects the characteristics of clusters: how numerous they are, how large they are, how rearranged they are and to what extent they are preserved from ancestor to descendant in a phylogenetic tree. We infer the latter property by dynamic programming optimization of the presence of individual edges at the ancestral nodes of the phylogeny. We apply our analysis to a set of genomes drawn from the Yeast Gene Order Browser.

Keywords

Dynamic Programming Candida Glabrata Ancestral Genome Maximum Bandwidth Ancestral Node 
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 2008

Authors and Affiliations

  • Qian Zhu
    • 1
  • Zaky Adam
    • 1
  • Vicky Choi
    • 2
  • David Sankoff
    • 1
  1. 1.Department of Biochemistry, School of Information Technology and Engineering, and Department of Mathematics and StatisticsUniversity of OttawaOttawaCanada
  2. 2.Department of Computer ScienceVirginia Tech.Blacksburg 

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