Here a question for immuno-informaticians among us (hope they are here at all):
We are attempting a reverse vaccinology approach on a fish-parasite (non-)model (Salmo salar and Lepeophtheirus salmonis). There we try to predict candidates from the proteome that would give good vaccine candidates. We found a pipeline, called vacceed, that might work for us. Reverse vaccinology approaches include predicting binding affinities of peptides or epitopes to the MHC-I and MHC-II classes using tools like IEDB. These tools have been mainly used sucessfully on mammalian data in my understanding, and therefore I have assumed so far that the results would not transfer well to a fish. Even in humans, the various different MHC alleles give very different binding affinities, and therefore MHC-I/II predictors (like IEDB, we intend to use the stand-alone Linux version) need the present alleles as input files. For salmon, i found a review on evolution of MHC alleles in teleost fish, but I am not quite sure how to prepare allele files from the presented information. Therefore my questions:
- How to prepare allele information for a fish as input to IEDB MHC predictors in the proper format?
- Will the result be any better than random? (guess this is hard to determine)
Example of an MHC-I allele file for cattle (from the vacceed manual):
BoLA-T2C,10 BoLA-T2C,11 BoLA-T2C,12 BoLA-T2C,13 BoLA-T2C,14 BoLA-T2C,8 BoLA-T2C,9
Example of an MHC-II allele file for humans
H2-IAb H2-IAd H2-IAs H2-IEd HLA-DPA1*01/DPB1*04:01 HLA-DPA1*01:03/DPB1*02:01