A method for comparing circular genomes from gene locations: application to mitochondrial genomes

Motivation: Data on the entire structures of organelle and bacterial genome s, most of which are known to be circular have accumulated at a rapid pace. This information enables us to utilize the locations of homologous gene pa irs for measuring the dissimilarity between complete genomic structures. Results: A macroscopic distance is presented for comparing circular genomes from their overall structures, on the basis of the locations of two pairs of homologous genes on the compared genomes. The novel aspect of our method is that the comparison between the genomes automatically reveals a relatio nship based on the information on all gene locations, by incorporating the mobility of each gene, which includes not only the gene order but also the relative location between gene pairs. The plausibility of the newly defined distances is evaluated by means of 44 mitochondrial genomes. The genome di stance shows high performance for quantitatively describing the differences between the gene organizations of the genomes.