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pVACvector is designed to aid specifically in the construction of DNA vector based personalized cancer vaccines. It takes as input either a pVACseq output tsv file or a FASTA file containing peptide sequences and returns a peptide ordering that minimizes the effects of junctional epitopes (that may create novel peptides) between the sequences. It does this by using the core pVACseq services to predict the binding scores for each junctional peptide separated by a spacer amino acid sequence that may help to eliminate junctional epitopes. The list of spacers to be tested is specified using the --spacers parameter. Peptide combinations without a spacer can be tested by including None in the list of spacers.

Peptide junctions are tested with each spacer in the order that they are specified. If a valid peptide ordering is found that doesn’t result in any well-binding junction epitopes, that ordering is returned. No other spacer are tested, even if they could potentially result in better junction scores. This reduces runtime. If no valid path is found, the next spacer in the input list is tested. The default spacer amino acid sequences are “None”, “AAY”, “HHHH”, “GGS”, “GPGPG”, “HHAA”, “AAL”, “HH”, “HHC”, “HHH”, “HHHD”, “HHL”, “HHHC”.

The final vaccine ordering is achieved through a simulated annealing procedure that returns a near-optimal solution, when one exists.