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

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4 Author(s)
Qian Zhu ; Dept. of Biochem., Univ. of Ottawa, Ottawa, ON ; Adam, Z. ; Choi, V. ; Sankoff, D.

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.

Published in:

Computational Biology and Bioinformatics, IEEE/ACM Transactions on  (Volume:6 ,  Issue: 2 )