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

Qian Zhu, Z. Adam, V. Choi, D. Sankoff
2009 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
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
more » ... ed 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.
doi:10.1109/tcbb.2008.121 pmid:19407346 fatcat:h7rlbyeosjgm7anc67aivhfyvm