Generalized Gene Adjacencies, Graph Bandwidth, and Clusters in Yeast Evolution

Authors:
Qian Zhu;Zaky Adam;Vicky Choi;David Sankoff
Affiliations:
University of Ottawa, Ottawa;University of Ottawa, Ottawa;Virginia Tech, Blacksburg;University of Ottawa, Ottawa
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2009

Citing 1
Cited 4

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IWOCA'10 Proceedings of the 21st international conference on Combinatorial algorithms
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APPROX'11/RANDOM'11 Proceedings of the 14th international workshop and 15th international conference on Approximation, randomization, and combinatorial optimization: algorithms and techniques
Bandwidth and low dimensional embedding

Theoretical Computer Science

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Abstract

We present a parameterized 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 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.