I want to map known epitopes in a protein sequence (antigen) to find out if it will evade the immune system or not. I found this website: http://www.iedb.org/ but not sure how to map so many small peptides to the protein sequence.
how many? If its under 5k then you can go here for MHC Class I processing predictions -
http://www.cbs.dtu.dk/services/NetCTLpan/ (actually it is synthesis of MHC Class I recognition + proteasome cleavage + transport to surface. Read more on the site)
and here for Class II -
In general, the CBS Predictions servers have other useful utilities (which can process multiple sequences) related immuno stuff.