An evaluation with 15 Staphylococcus aureus and 4 Escherichia coli O157:H7 genomes with default parameters (95% minimal sequence similarity, not >95% similar to another ORF within the same chromosome (percent identity and overlap), 100% presence in the investigated genomes/sequences) yielded 1,131 and 3,200 core ORFs for S. aureus and E. coli, respectively.