D: Natural parameter values for generalized gene adjacency

Abstract. Given the gene orders in two modern genomes, it may be dif-ficult to decide if some genes are close enough in both genomes to infer some ancestral proximity or some functional relationship. Current meth-ods all depend on arbitrary parameters. We explore a two-parameter class of gene proximity criteria, and find natural values for these pa-rameters. One has to do with the parameter value where the expected information contained in two genomes about each other is maximized. The other has to do with parameter values beyond which all genes are clustered. We analyse these using combinatorial and probabilistic argu-ments as well as simulations.