title: Generalized gene adjacencies, graph bandwidth, and clusters in yeast evolution.
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.
authors.affiliation: Department of Biochemistry, University of Ottawa, Ottawa, ON, Canada. qzhu012@uottawa.ca
authors.forename: Qian
authors.initials: Q
authors.lastname: Zhu
authors.forename: Zaky
authors.initials: Z
authors.lastname: Adam
authors.forename: Vicky
authors.initials: V
authors.lastname: Choi
authors.forename: David
authors.initials: D
authors.lastname: Sankoff
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003198:Computer Simulation; D019143:Evolution, Molecular; D005800:Genes, Fungal; D014644:Genetic Variation; D016681:Genome, Fungal; D008957:Models, Genetic; D015233:Models, Statistical; D005810:Multigene Family; D010802:Phylogeny; D015003:Yeasts / Q000235:genetics*