Figure 1.

Our method of analyzing protein phylogenetic profiles is illustrated schematically for the hypothetical case of four fully sequenced genomes (from E. coli, Saccharomyces cerevisiae, Haemophilus influenzae, and Bacillus subtilis) in which we focus on seven proteins (P1–P7). For each E. coli protein, we construct a profile, indicating which genomes code for homologs of the protein. We next cluster the profiles to determine which proteins share the same profiles. Proteins with identical (or similar) profiles are boxed to indicate that they are likely to be functionally linked. Boxes connected by lines have phylogenetic profiles that differ by one bit and are termed neighbors.