The HIV-1 HXB2 sequence for Env, Pol, Vpu, Rev, Tat, Vif, Vpr, p17, p24 and p2p7p1p6 and the HIV-1 clade B consensus sequence for Nef (due to a stop codon in HXB2-Nef) were downloaded from the Los Alamos database (www.hiv.lanl.gov). There was also one stop codon in HXB2 sequence for TAT, however, no TAT peptides were predicted to be HLA-A2 epitopes and thus the stop codon did not interfere with our results. Out of 3,063 HIV nonamers, 91 were predicted to be HLA-A2 epitopes using NetCTL version 1.2 [25, 26] and default selection threshold (0.75). NetCTL predicts the level of antigen presentation by combining three separate predictions of: proteasomal cleavage, TAP affinity and MHC biding. Four out of the 91 predicted HIV epitopes were found to be immunogenic for other supertypes than HLA-A2 and were filtered out. These were: QLQARILAV, RILAVERYL (class II, DPW4.2), TLYCVHQRI (HLA-A11) and SINNETPGI (HLA-A25). Of the remaining 91-4 = 87 peptides, 33 were confirmed HLA-A2 epitopes by cross-referencing the records of the LANL CTL epitope summary table (downloaded December 2006). Thus, the epitope prediction resulted in the identification of 87 possible HLA-A2 restricted HIV epitopes where 33 (38%) were confirmed and 54 (62%) were not.