biostudies-literatureBjerregaard AMBreast Cancer Research FoundationNovo NordiskKræftens BekæmpelseDet Frie Forskningsråd1123-1130https://www.ebi.ac.uk/biostudies/studies/S-EPMC11028452biostudies-literatureUnknown66(9)Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the mutant peptide extractor and informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tumCancer immunology, immunotherapy : CIIMuPeXI: prediction of neo-epitopes from tumor sequencing data.PMC11028452R72-A46181331-0028316854Szallasi ZHadrup SRBjerregaard AMNielsen MEklund ACfalseMuPeXI: prediction of neo-epitopes from tumor sequencing data.Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the mutant peptide extractor and informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tum2017-01-01T00:00:00Z2017 Sep2025-04-22T20:43:34.939Z2025-04-06T03:14:49.999ZS-EPMC110284522842906910.1007/s00262-017-2001-3