Flowchart showing the calculation of linear and circular Zaslaver scores. (i) Given a species with 2 operons containing genes of interest, each linear permutation of gene order can be assessed using the Zaslaver score. (ii) For the gene order A, D, C, B, the genes in the observed operons are first rearranged according to this permutation. (iii) The Zaslaver score is calculated for each operon, then the scores for all operons are summed. For the operon containing genes A, C, B, it can be seen that there is 1 skipped step (gene D) according to the permutation being tested, resulting in a score of 1 for this operon. For the operon containing genes D and C there are no skipped steps, resulting in a score of 0. (iv) The score can be extended to account for circular permutations. Taking each gene in the circular permutation in turn as the starting gene, the linear score for each operon is calculated. The minimum score of these permutations is taken for each operon, and these are then summed to give a final circular Zaslaver score.