Methods:

Gene cluster data were generated using the BugSpray Genome Comparison Tool which enables the researcher to identify and map orthologous clusters of genes between two genomes. This is a multi-step process. First, BLAST data are generated to determine significantly similar proteins; only orthologs with BLAST E-values under e-04 are included. Next, bi-directional best hits in BLAST are determined for each gene; e.g. if PG0211 has a best hit to (is most similar to) CT568, and CT568 has a best hit to PG0211, the pair is considered a bi-directional best hit. All other orthologs are excluded. This prevents one gene from hitting to multiple, less similar, genes in the other genome and helps to avoid false identification of potential operons. BugSpray then addresses proximity. All genes with bi-directional best hits that are more than a given number (user-specified) of base pairs apart are excluded. Finally, only clusters larger than a certain size (user-specified) are included in the output map and data table. Porphyromonas gingivalis was compared against Chlamydia trachomatis, Chlamydia pneumoniae, Treponema pallidum, Ureaplasma urealyticum, Neisseria meningitidis (strains MC58 and Z2491), Haemophilus ducreyi, Streptococcus pyogenes, and Escherichia coli. Gene clusters revealed through the above process are then analyzed to determine whether or not they are conserved between bacterial genomes. Conserved gene clusters are found in at least 3 bacterial genomes.