Comparing bacterial genomes from linear orders of patterns

We compare complete genomes from common words denoted MUMs for maximum unique matches. They allow to transform each genome into a linear order. We first evaluate the minimum length of a MUM shared by two genomes to be significant. Secondly, we compute maximal common chains of elements, that are in the same order in genomes. From these chains we define conserved genome segments as long DNA fragments having MUMs in the same order and with a bounded gap length between them. The resulting small number of segments allow to detect main evolutionary events as reversal or transposition of these fragments.