Generalized gene adjacencies, graph bandwidth and clusters in yeast evolution

Authors:
Qian Zhu;Zaky Adam;Vicky Choi;David Sankoff
Affiliations:
Department of Biochemistry, School of Information Technology and Engineering and Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada;Department of Biochemistry, School of Information Technology and Engineering and Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada;Department of Computer Science, Virginia Tech., Blacksburg, VA;Department of Biochemistry, School of Information Technology and Engineering and Department of Mathematics and Statistics, University of Ottawa, Ottawa, Canada
Venue:
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Year:
2008

Citing 3
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Abstract

We present a parametrized definition of gene clusters thatallows us to control the emphasis placed on conserved order within acluster. Though motivated by biological rather than mathematical considerations,this parameter turns out to be closely related to the maximumbandwidth parameter of a graph. Our focus will be on how thisparameter affects the characteristics of clusters: how numerous they are,how large they are, how rearranged they are and to what extent theyare preserved from ancestor to descendant in a phylogenetic tree. Weinfer the latter property by dynamic programming optimization of thepresence of individual edges at the ancestral nodes of the phylogeny. Weapply our analysis to a set of genomes drawn from the Yeast Gene OrderBrowser.