This chapter explains computer techniques for comparing genes, proteins, or genomes of methicillin-resistant Staphylococcus aureus (MRSA). In the principle methodology for comparative genomics, first researchers obtain the data of DNA sequences and phenotypes for various strains of interest, and from those they infer what difference/similarity in sequences results in what difference/similarity in phenotypes. Usually, the obtained hypothesis provides guidance for the succeeding biological experiments, such as producing knockout strains or conducting transcriptome or proteome analysis, which examine the hypothesis. Even for physicians and experimental researchers, these computer-aided researches would be needed in order to understand the physiological characteristics and pathogenic abilities of the MRSA that they deal with in this “genome era.” This chapter involves no experiments and is confined to computer analysis. We explain methods for extracting the difference/similarity between sequences of nucleotide, amino acid, or even the whole genomes of bacteria. We also introduce how to compare the pathways between strains that possess different sets of genes.