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EpitopePrediction

Predicts binding of 9- to 12-mer peptides to MHC class I molecules using the stabilized matrix method (B. Peters and colleagues). Can predict binding for several alleles from humans (HLA A/B), mice (H-2), chimpanzees (Patr A/B), and rhesus macaques (Mamu A/B).

License

This package is licensed under a CC BY-NC-SA 4.0 license. This means it is free for use for non-commercial purposes (such as academic research). Companies interested in using this package should contact Bjoern Peters.

Example

# Install the package
devtools::install_github("jtextor/epitope-prediction")

# Load the package
library( EpitopePrediction )

# This is the CORE protein from the Hepatitis C virus reference sequence available
# at https://hcv.lanl.gov/content/sequence/LOCATE/locate.html
hcv.core <- paste("MSTNPKPQRKTKRNTNRRPQDVKFPGGGQIVGGVYLLPRRGPRLGVRATRKTSERSQPRGRR",
	"QPIPKARRPEGRTWAQPGYPWPLYGNEGCGWAGWLLSPRGSRPSWGPTDPRRRSRNLGKVIDTLTCGFADLMGYIP",
	"LVGAPLGGAARALAHGVRVLEDGVNYATGNLPGCSFSIFLLALLSCLTVPASA",sep="")

# Predict 9-mer binders to human HLA-A02:01
binders( hcv.core, "HLA-A-02:01", 9 )