Fig. 7

Exemplification of the CUPP clustering dissimilarity score. Determination of the dissimilarity score between two protein domain regions during CUPP clustering exemplified as two scenarios: one of high similarity between the two proteins (A and B) and one with a low similarity. The thick black horizontal line represents the amino acid sequence of the two target proteins. The conserved peptides found in protein A are indicated individually by the short red line above the protein. Similarly, beneath protein B, the presence of conserved peptides of protein B is shown as short blue lines. The subset of conserved peptides found in both protein A and protein B is represented by the short black lines between the two proteins. To determine the dissimilarity, the number of different positions covered by the conserved peptides is determined for each of the three colors of peptides indicated by the numbers (blue, red, and black). The dissimilarity score equals one minus the number of black peptide start positions divided by two times the maximum of the number of peptide start positions of the red or the blue peptides