Additional file 1:

Table S1 – Epitopes included in the study. There were 218 epitopes in the "best defined CTL epitopes list" by Frahm et al. (2007). From this, 29 epitopes were removed from the 62-all data set because they did not satisfy the inclusion criteria. Additionally, one epitope from the 44-non-CRFs data set and 29 epitopes from the 18-CRFs data set were removed because of the inclusion criteria.

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Additional file 2:

Table S2 – Number of epitopes included in the study. The number of epitopes included in the study as well as epitopes found in association rules in each gene.

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Additional file 3:

Table S3 – Unique epitope associations in the 62-all data set. Each row represents one epitope association. Associated epitopes in each association are shown in adjacent columns. Presence of the association in other data sets is represented by 1 in respective columns. There are 484 unique associations in the 62-all data sets. Among them, 172 associations are present in the 44 – non-CRFs data set and 102 associations are present in the 18 – CRFs data set. The yellow color marks presence of the epitopes from all three genes in the 62-all data set. There are 23 associations of that kind.

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Additional file 4:

Table S4. Stage of HIV-1 infection where the epitopes have been shown to be immunogenic, if known.

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