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Welcome to the systeMHC wiki!

Brief description of workflow:

• 2-3 search engines :comet, myrimatch, (msgf+) for identification of MHC peptides
• TPP - peptide prophet and iprophet for rescoring and fdr estimation
• netMHC3.4 and netMHCcons for verification and annotation of pepites
• recomputation of fdr
• spectrast for swath library creation

The workflow is implemented using the applicake plumbing toolkiet

Open questions :

• is visualization of results as described in the eLife paper essential?
• how does the output of the workflow looks like:
  • meta information about sample
  • annotation of the identified pepites

getting all the required code

sudo apt-get install git

git clone https://github.com/systemhc/systemhc
git clone https://github.com/SysteMHC/SysteMHC_Binaries
git clone https://github.com/SysteMHC/RnetMHC
git clone https://github.com/SysteMHC/SysteMHC_Data
git clone https://github.com/applicake-tools/applicake
git clone https://github.com/applicake-tools/toolscake

at a later stage we might use git submodules

Related projects:

applicake

Related projects

immuneepitope

iedb