MuPeXI: Mutant Peptide eXtractor and Informer

Given a list of somatic mutations (VCF file) as input, MuPeXI returns a table containing all mutated peptides (neo-peptides) of user-defined lengths, along with several pieces of information relevant for identifying which of these neo-peptides are likely to serve as neo-epitopes.

Authors:

Anne-Mette Bjerregaard and Aron C. Eklund

License:

To be determined, but certainly free for academic use.

Citation:

Bjerregaard AM, Nielsen M, Hadrup SR, Szallasi Z, Eklund AC.
MuPeXI: Prediction of neo-epitopes from tumor sequencing data.
Cancer Immunol Immunother. 2017 Apr 20. doi: 10.1007/s00262-017-2001-3. [Epub ahead of print]
PubMed ID: 28429069
You can read the paper here: http://rdcu.be/rwVP

Web server:

For limited data, MuPeXI can be run on our web server

Dependencies

Hardware:

MuPeXI currently runs only on x86_64 machines running Linux or Darwin.

Required software:

• Python 2.7
• NetMHCpan 3.0
• Variant Effect Predictor (VEP)

Required Python modules:

• Biopython
• numpy
• pandas

Note: These modules are already included if using Python through Anaconda.

Optional software, required only for liftover from HG19

• Picard tools
• Java 8

Installation

1. Install all software listed above.

2. Download or clone the MuPeXI repository to your local system

    git clone https://github.com/ambj/MuPeXI.git
   

3. Obtain the reference files from GRCh38. These include cDNA, peptide and COSMIC files; see the References section in the user manual for a detailed description.

4. Fill in the config.ini file

   • Provide the full path to NetMHCpan 3.0 and VEP.
   • Provide the full path to the reference files:
     • cDNA
     • peptide
     • COSMIC

   Additional peptide references and liftover paths can be provided in the config.ini file; see the user manual for detailed information. Instructions on how to fill in the config.ini file are found within the file. config.ini is automatically found if it is in the same directory as MuPeXI.py script, but it can also be placed elsewhere and specified by the -c option.

Usage

Here is a simple example in which somatic mutation calls and gene expression data are provided, and MHC binding is predicted for HLA types HLA-A01:01 and HLA-B08:01.

path/to/MuPeXI.py -v mutations.vcf -a HLA-A01:01,HLA-B08:01 -e expression.tsv

MuPeXI can be used for both peptide extraction, giving immunogenicity information for peptide selection (the default), and for generation of a FASTA-formatted mutant-peptide file suitable for input to mass spectrometry peptide search software (with the -f option).

All options can be displayed using the usage information with the -h option:

path/to/MuPeXI.py -h

User Manual

For detailed information about usage, input and output files, test examples and data preparation read the MuPeXI User Manual

FAQs

• We pronounce it moo-PECKS-ee

Contact

Anne-Mette Bjerregaard
[email protected]

or

Aron Charles Eklund
[email protected]

Department of Bio and Health Informatics
Technical University of Denmark
http://www.bioinformatics.dtu.dk/english

Algorithmic Flow Chart