Protein signature prediction and SAP methods have previously been described in detail (6) . The following briefly describes the procedure. First, target genomes are aligned using WGASA. A set of gene (start, end) pairs for both the plus and minus strands relative to the reference genome is required. This implies that coding frames for the translation of nucleic acid codons into amino acids for each protein of the target organism's genome have been correctly determined. From the aligned genomes, nucleotide codons are translated into amino acid sequence based on the gene locations, and conserved strings of six or more amino acids among all the target genomes are recorded. These conserved fragments are then compared with the NCBI GenBank non-redundant (nr) database of amino acid sequences, unveiling peptides that are unique to the target species. For our computations, we require that if a peptide signature is longer than six amino acids, then every sub-string of length six amino acids is also conserved and unique. There may be many conserved and unique peptide signatures on the same and on different proteins. The resulting conserved, unique peptides that are at least six amino acids long from open reading frames are considered to be protein signature candidates.