ImmunePredictor is a pipeline developed in Python that predicts peptide cleavage, peptide-MHC affinity, stability, immunogenicity and self similarity (to human proteome) scores for human MHC class I.
The pipeline require the following external software tools:
- NetChop 3.1 - Download: http://www.cbs.dtu.dk/services/NetChop/ - Note that we do not support the OSX version
- NetMHCpan 3.0 - Download: http://www.cbs.dtu.dk/services/NetMHCpan/
- NetMHCstabpan 1.0 - Download: http://www.cbs.dtu.dk/services/NetMHCstabpan/
Install and test:
- Download the "WP3-ImmunePredictor/src/", "WP3-ImmunePredictor/data/" and "WP3-ImmunoPredictor/test/" directories. Make sure that "src", "data" and "test" are located in the same directory.
- Download "data.tar.gz" from: http://tbb.bio.uu.nl/ewald/immunePredict/. Unpack the content into the "data" folder
- Install NetChop, NetMHCpan and NetMHCstabpan
- Open "WP3-ImmunePredictor/src/test_example.py"
- In "test_example.py", locate the "toolParams" class and set the absolute paths for the netChop, netMHCpan and netMHCstabpan binaries. Note that netChop also requires an environment directory
- Run "test_example.py" to test the pipeline on an example input file from WP3-ImmunoPredictor/test/
- See "test_example.py" for usage instructions