Given the peptides (T-cell epitopes) PolyCTLDesigner selects flanking sequences to optimize TAP-binding and joins resulting oligopeptides into a polyepitope in a way providing efficient liberation of potential epitopes by proteasomal and/or immunoproteasomal processing and minimizing the number of junctional epitopes. For constructing polyepitopes PolyCTLDesigner utilizes known amino acid patterns of proteasome cleavage and TAP-binding specificity. PolyCTLDesigner is also able to choose antigenic peptides covering selected HLA repertoire with desired redundancy rate. Given the antigen sequences PolyCTLDesigner is also able to select T-helper epitopes. For predicting T-cell epitopes it uses TEpredict.
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