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pVACvector is designed to aid specifically in the construction of DNA-based cancer vaccines. It takes as input either a pVACseq output tsv file or a fasta file containing peptide sequences and returns an 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. It also tests junctions with spacer amino acid sequences that may help to reduce reactivity. These spacer amino acid sequences can be “HH”, “HHC”, “HHH”, “HHHD”, “HHHC”, “AAY”, “HHHH”, “HHAA”, “HHL” or “AAL. The final vaccine ordering is achieved through a simulated annealing procedure that returns a near-optimal solution, when one exists.