Neisseria meningitidis is the agent of invasive meningococcal disease,including cerebral meningitis and septicemia.Because the diseases caused by different clonai groups (sequence types) have their own epidemiological characteristics,it is important to understand the differences among the genomes of the N.meningitidis clonal groups.To this end,a novel interpretation of a structural dot plot of genomes was devised and applied;exact nucleotide matches between the genomes of N.meningitidis serogroup A strain Z2491 and serogroup B strain MC58 were identified,leading to the specification of various structural regions.Known and putative virulence genes for each N.meningitidis strain were then classified into these regions.We found that virulence genes of MC58 tend more to the translocated regions (chromosomal segments in new sequence contexts) than do those of Z2491,notably tending towards the interface between one of the translocated regions and the collinear region.Within the collinear region,virulence genes tend to occur within 16 kb of gaps in the exact matches.Verification of these tendencies using genes clustered in the cps locus was sufficiently supportive to suggest that these tendencies can be used to focus the search for and understanding of virulence genes and mechanisms of pathogenicity in these two organisms.