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MuPeXI 1.2.0 Server

Prediction of neo-epitopes from tumor sequencing data

Mutant peptide extractor and informer (MuPeXI)

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

Instructions Output format Article abstract


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:

Select HLA locus

Select allele (max 20 per submission) or type allele names (e.g. HLA-A01:01) separated by commas (and no spaces). Max 6 alleles per submission)

For a list of allowed allele names click here List of MHC allele names.

Select peptide length (multiple lengths are possible):

Output FASTA file with long peptides - mutation in the middle 

Submit HG19-aligned VCF file (liftover to GRCh38 will be performed) 

Max 6 MHC alleles per submission.

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


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 NetMHCpan; for publication of results please cite NetMHCpan in addition to MuPeXI.

  • NetMHCpan - MHC class I binding prediction beyond humans
    Ilka Hoof, Bjoern Peters, John Sidney, Lasse Eggers Pedersen, Ole Lund, Soren Buus, and Morten Nielsen
    PMID: 19002680
    Full text
  • NetMHCpan, a method for quantitative predictions of peptide binding to any HLA-A and -B locus protein of known sequence.
    Nielsen M, Lundegaard C, Blicher T, Lamberth K, Harndahl M, Justesen S, Roeder G, Peters B, Sette A, Lund O, Buus S.
    PMID: 17726526
    Full text


MuPeXI is available on GitHub.


Scientific problems: