MuPeXI 1.2.0 Mouse Compatible Server

Prediction of neo-epitopes from murine sequencing data

Mutant peptide extractor and informer (MuPeXI)

Extracts user defined peptides lengths around missense variant mutations, indels and frameshifts from a VCF file obtained from murine sequencing data. Information from each mutation is annotated together with the mutant and normal peptides in the file output.

Instructions Output format Article abstract

SUBMISSION

Submit a VCF file (example of a VCF):
Please ensure your VCF file has been filtered to remove non-somatic variants!

Submit an expression file - optional (example of an expression file):

Select whether expression data is quantified at the level of genes or transcripts:


Running analysis with mus musculus reference
for species specific analysis of BALB/cJ or C57BL/6 see MuPeXI GitHub page

Select H2 locus

Select allele (max 6 per submission) or type allele names (e.g. H-2-Db) separated by commas (and no spaces). Max 6 alleles per submission)



Select peptide length (multiple lengths are possible):


Output FASTA file with long peptides - mutation in the middle 


Restrictions:
Max 6 MHC alleles per submission.

Confidentiality:
The files are kept confidential and will be deleted after processing.


CITATIONS

For publication of results, please cite:

  • MuPeXI: Prediction of neo-epitopes from tumor sequencing data
    Anne-Mette Bjerregaard, Morten Nielsen, Sine R. Hadrup, Zoltan Szallasi, and Aron C. Eklund
    Cancer Immunol Immunother. 2017 Apr 20. doi: 10.1007/s00262-017-2001-3.
    PubMed ID: 28429069
    Full text

MuPeXI relies on binding predictions from NetH2pan; for publication of results please cite NetH2pan in addition to MuPeXI.

  • NetH2pan: A Computational Tool to Guide MHC peptide prediction on Murine Tumors
    Christa I. DeVette, Massimo Andreatta, Wilfried Bardet, Steven J. Cate, Vanessa I. Jurtz, Kenneth W. Jackson, Alana L. Welm, Morten Nielsen, William H. Hildebrand
    Cancer Immunology Research (2018) DOI: 10.1158/2326-6066.CIR-17-0298
    Full text  
  • NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data
    Vanessa Jurtz, Sinu Paul, Massimo Andreatta, Paolo Marcatili, Bjoern Peters and Morten Nielsen
    The Journal of Immunology (2017) ji1700893; DOI: 10.4049/jimmunol.1700893
    Full text   [PDF]


PORTABLE VERSION

MuPeXI is available on GitHub.


GETTING HELP

Scientific problems: