Does mpg support no cleavage?

[lydiayliu]

But for immunopeptidome, we known those peptides have affinity to HLA, so moPepGen would be a perfect fit for generating custom DB to search for it.

I've been wondering about what you said here. I think some tweaks are required for mpg to generate neoantigens. I just realized that I used trypsin as the enzyme for calling neoantigens. Even though MHCFlurry can chop the peptides generated by mpg into arbitrary shorter peptides (could be bad if the fragments dont actually contain the variant), it would probably be more ideal to have a "no cleavage" or "native peptides" mode for mpg (and turn off the chopping function in MHCFlurry if possible :P)

[zhuchcn]

Not impossible. Instead of creating the peptide cleavage graph, we can create a peptide kmer graph. But this would need a lot of work, because we'll have to create a new model for this kind of graph.

[lydiayliu]

Why don't we just forget about the cleavage graph and go straight from the peptide variant graph? Traverse the graph for each length of peptide, or each "frame" of peptide

[zhuchcn]

I think that should work! We then don't need to worry about the miscleavages. Just need to write a new traverser.