Longest Common Circular Chains of Maximal Unique Matches between Bacterial Genomes

The aim of this study is to compare complete genomes to identify preserved large DNA fragments in order to analyse evolution process. For this purpose, we propose an efficient method to identify conserved regions between multiple genomes. We first transform each complete genome into a permutation of Maximal Unique Matches (MUMs). Secondly, we compute the longest common sequence of MUMs in the same order in all the genomes. This permits to define conserved genome segments as long DNA fragments having MUMs in the same order and to analyse evolution events as reversal or transposition of this fragments.Finally, we propose some genomic distances based on MUMs and conserved genome segments length and number.