Fig. 5.

Comparison between experimentally used spacer sequences and in silico designed spacer sequences for the multiepitope polypeptide proposed by Levy et al. Red bars represent predicted epitopes and the intensity indicates overlapping epitopes at that position. The blue rectangles represent predicted C-terminal cleavage sites. Spacer sequences are marked in red. A tick indicates the start position of a predicted nine-mer epitope. Epitope and cleavage site predictions were performed with SYFPEITHI and PCM, respectively. A peptide was predicted as an epitope if its prediction score was equal to or above a threshold of 20 (default threshold of SYFPEITHI). A cleavage site was said to be cleaved if the predicted PCM score was above zero. An epitope was defined as recovered if both preceding and succeeding cleavage sites were predicted to be cleaved