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This is a set of scripts that together predict MHC ligands and output a fasta file to be used for downstream mass spectrometry based searches.
This is second version of SpectMHC software (version 1: https://github.com/Prathyusha-konda/SpectMHC)
MHC-I Ligand Discovery Using Targeted Database Searches of Mass Spectrometry Data: Implications for T-Cell Immunotherapies (https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00971)
bash ./spectmhc.sh [-r] [-s] <NetMHC folder> <MHC version> <input fasta> <binding cutoff> <allele> <length of peptide> <number of split files>
Example: bash ./spectmhc.sh -s /home/prathyusha/NetMHC_4.0_for_Linux/netMHC-4.0 4.0 human_proteins.fasta 2 HLA-A0301 10
| position | description |
|---|---|
| NetMHC folder | path to NetMHC folder |
| MHC version | input the version of netMHC 3.4/4.0/pan |
| input fasta | input protein data in fasta format |
| binding cutoff | cutoff to be used (rank for netmhc 4.0/pan, binding affinity for 3.4) |
| allele | MHC allele to predict |
| length_of_peptide | Length of peptides to predict, if multiple, please seperate by ','. Ex: 8 or 8,9,10 |
| number_of_split_files | only works if -s is selected. enter a numeric value, such that every split file has between 1000-2000 sequences. Insert 0 if not using this. |
-h -> help
-r -> save raw netmhc output
-s -> split input fasta file
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Clone this repository by running one of the following:
git clone [email protected]:Prathyusha-konda/SpectMHC-v2.gitif you use ssh authenticationgit clone https://github.com/Prathyusha-konda/SpectMHC-v2.gitotherwise
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Dependencies NetMHC (ligand prediction):
- NetMHCpan 4.0: http://www.cbs.dtu.dk/services/NetMHCpan/
- NetMHC 4.0: http://www.cbs.dtu.dk/services/NetMHC-4.0/
- NetMHC 3.4: http://www.cbs.dtu.dk/services/NetMHC-3.4/
- Python (helper code): https://www.python.org/download/releases/2.7/
- A targeted database of MHC ligands in fasta format to be used for mass spectrometry searches.