Putative antigenic peptides were predicted using the method of
Kolaskar and Tongaonkar, as implemented in EMBOSS (antigenic).
Each predicted epitope has an associated score based on the
physicochemical properties of the aminoacid residues. A
cumulative antigenicity score was calculated as the sum of
scores of all predicted epitopes in the protein. A normalized
antigenicity index was calculated as the ratio of this
cumulative score over the protein length. Finally, for each of
these normalized antigenicity index values we calculated the
percent of proteins for each genome that fall below it. Thus a
protein with an antigenicity index percentile of 80 means
that 80% of the proteins of the genome have a lower normalized
antigenicity index score (i.e. this protein is amongst the top 20%
of the proteins in these genome in terms of predicted
antigenicity).
