The present invention generally relates to a method for designing recombinant poxviruses for therapeutic vaccines, i.e., personalized
cancer vaccines, wherein the recombinant poxviruses comprise one or more expression cassettes, each expressing a fusion of multiple peptides (i.e., neopeptides), the method comprising performing, by a
processing means (11) of a
server (1), the following steps: (a) selecting a first subset of candidate peptides, wherein the candidate peptides exhibit a membrane-spanning
score below a TMS threshold; (b) determining an optimal distribution of the candidate peptides from the first subset into one or more expression cassettes from among a plurality of possible distributions, wherein, if more than one
expression cassette is present, the optimal distribution exhibits the lowest range of hydropathic scores of the two or more expression cassettes; (c) determining, for each
expression cassette, an optimal slot assignment of the candidate peptides as a function of the cassette's slot occupancy rules, in order to select the
peptide fusion with the lowest TM
score; and (d) determining
a DNA transfer sequence comprising the
nucleotide sequence of the one or more expression cassettes to generate the recombinant poxvirus.