I have no idea how these epitope prediction software's do work but I think using them will be somehow beneficial rather than designing primers blindly for the peptide synthesis. Before I use any epitope prediction software and start designing primer against predicted epitope, I would like to read your logical replies, your suggestion that how using epitope prediction software would help me.
Nowadays we have an increasing fold of papers working on developing peptide based vaccines with the aid of epitope prediction algorithms, may be the most influential example is against ebola and zika viruses, and we can see that assays always confirm these predictions, you can review that article on the accuracy of epitope prediction algorithms and how they are cost and time effective than before http://www.sciencedirect.com/science/article/pii/S1532046414002330
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