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artyomovlab / hmmhc

MHC class II binding prediction
MIT License
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Peptide length limitation #4

Open DivyaRavichandar opened 4 years ago

DivyaRavichandar commented 4 years ago

Currently this code works for peptides in 12 -24 AA range. it appears this in enforced for the percentile calculation. Would removing this limitation still allow for the log odd calcualtions?

ikizhvatov commented 4 years ago

Yes, technically log odds is computable also outside of this range.

DivyaRavichandar commented 4 years ago

Thanks. Since the tool currently is restricted to this range. IF I were to use this to calcualte log odds for longer peptides (say 10 - 40 aa).

Would I simply take out the length checks on line 86 in the hmmhc.py script?

ikizhvatov commented 4 years ago

Yes, it should work. Beware though that for the lengths outside of the range the predictions may be less reliable, as the training set contained mostly lengths 12-24.