I am trying to match epitopes from a database to a protein sequence. I have 400+ epitopes (a lot of overlap of course) that need mapped to one protein. What is the easiest way to do this? I downloaded the standalone BLAST on recommendation of my adviser but can't figure out what format the input file should be (if I create a database with only the sequence?). I also have R studio if there is an easier way to do it there. I just need the location of each epitope so I can map them.

Thank you