In my analysis I took a look at KM233100.1 and protein AIG96469.1. I used the IEDB MHC-I processing predictions tool. The MHC-I processing predictions tool takes a look at a protein sequence and gives you predicted peptide affinity for MHC class 1. According to the prediction tool there are three likely epitope candidates. An IC50nM score of less than 50 indicates high affinity, scores between 50 and 500 have intermediate affinity, and sequences between 500 and 5000 have low affinity. As you can see in the picture there are three peptides with an IC50nM of less than 50. Although this isn’t a guarantee that these are the only epitope candidate. Some peptides have a low affinity but are still epitopes. Further analysis of the first peptide in the picture shows that this is already a known epitope with the actual epitope being one AA longer. The second prediction is also a known epitope that is one AA longer than the prediction. Finally the last predicted epitope is also an already known epitope but this time the prediction was 100% correct. All three epitopes where identified in the same paper. This analysis to me shows that the prediction tool is a doing a good job at predicting the correct affinity for peptides. This would be a very powerful tool when conducting research on finding epitopes. You would cut out a lot of the guess work and give a very good foundation to build upon. Another analysis by the Virus Pathogen resource shows a possible 119 predicted epitopes. While the MHC-I processing predictions tool only shows 17 peptides with even intermediate affinity. Further experimental analysis is definitely needed to find all the correct epitopes.
michelconn 