Figure 4.

Immunogenicity Scores for TMHMM dataset and definition of valid epitopes. (A) All sequences within each cluster were submitted to MHC II immunogenicity scoring, to all tested alleles. Sequences with percentile score lower than 0.05 were selected. Cluster immunogenicity is given by the mean distribution of all scored epitopes under this value, for all proteins. Highly immunogenic clusters were defined as those with a mean score lower than 0.02 (black dots). (B) Example of a homolog from cluster 71 (Cytochrome c subunit III protein). Immunogenicity prediction defined four regions of this protein to contain possible epitopes (Before panel, in pink). As shown in the figure, three of those regions are within the transmembrane domain. Protein topology alignment allowed the removal of such regions, which were then considered invalid epitopes (After panel). (C) Valid epitopes were then checked if they are conserved within all homologs of its cluster. Most clusters contained conserved identical epitopes in all homologs (count 7, pink). Epitopes present in 5 or less components of the cluster were not considered for further analysis.