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Assembles a set of epitopes into an optimal string-of-beads polypeptide vaccine construct. It consumes a peptide list and generates a traveling salesman problem (TSP) instance as described in (Toussaint et al., 2011). Each node of the underlying fully connected graph represents a peptide, each edge’s weight expresses the cleavage probability of the connected epitopes predicted by the user specified cleavage site prediction model.
(Toussaint et al., 2011) Universal peptide vaccines - optimal peptide vaccine design based on viral sequence conservation. Vaccine.
(Schubert et al., 2017) ImmunoNodes - graphical development of complex immunoinformatics workflows. BMC Bioinformatics.