Comparison between our predictor (MixMHCpred1.0) and existing tools.

<p><b>A</b>: Fraction of the true positives among the top 1% predictions (PP1%) for the naturally presented HLA-I ligand identified in mono-allelic cell lines, with 99-fold excess of decoy peptides. Of note, PP1% is equivalent to the both Precision and Recall, since the number of actual positives is the same as the number of predicted positives. <b>B-C</b>: Graphical representation of results in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005725#pcbi.1005725.t001" target="_blank">Table 1</a> and Table C in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005725#pcbi.1005725.s001" target="_blank">S1 Supporting Information</a>. Panel B shows the AUC values and panel C the fraction of neo-antigens predicted in the top 1% of predictions (which typically corresponds to what is experimentally tested for immunogenicity). <b>D-E</b>: Predictions of Cancer Testis Antigens from the CTDatabase. Panel D shows AUC values and panel E shows PP1%. Truncated y-axes are explicitly indicated.