Epitope prediction - what is best input?

Question

[heir_of_isildur88]

Hi all, I am going to perform epitope binding prediction using NetMHC. What I want to know is what is the most suitable input to use? Do I use: 1) The peptide sequence obtained from Ensembl - some of them are 3' incomplete though; OR 2) The peptide sequence obtained from translating the coding sequences of the said gene obtained from Ensembl - this way, you get the complete peptide, but some of them are not the same with the ones obtained from (1), maybe due to insertions / deletions in the transcript.

Thank you.