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Published in:
2008 | OriginalPaper | Chapter
Generalized Gene Adjacencies, Graph Bandwidth and Clusters in Yeast Evolution
Authors : Qian Zhu, Zaky Adam, Vicky Choi, David Sankoff
Published in: Bioinformatics Research and Applications
Publisher: Springer Berlin Heidelberg
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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.