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)


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.


Dynamic Programming Candida Glabrata Ancestral Genome Maximum Bandwidth Ancestral Node 
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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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