Counting approximate breakpoint medians of random genomes

Abstract

Unsigned linear unichromosomal genomes with genes labeled 1, . . . , n are represented by permutations of these labels, whose adjacencies are the unordered pairs of genes occurring consecutively. The breakpoint distance counts the adjacencies of one genome that are absent from the other, and a breakpoint median minimizes the total breakpoint distance to a given set of genomes. Deciding whether a permutation is a median often requires a minimization over the whole symmetric group, which makes the median set resistant to exact counting. We replace this global condition by a local one: a c-approximate median is a genome having at most c adjacencies absent from all the input genomes. For a fixed genome we introduce its approximate median inverse, the set of ordered k-tuples of genomes ad- mitting it as a c-approximate median, and we construct and count this set explicitly. For k genomes chosen uniformly and independently at random, this gives the probability that a given genome is a c-approximate median and the expected number of such approximate medians. The relaxation is not only technical: approximate medians and near-optimal genomes co- incide up to a shift of the tolerance that remains bounded in probability as the number of genes grows. Finally, we derive an explicit upper bound on the probability that a given genome is an exact median, and on the expected number of exact breakpoint medians.