A Computational Pipeline for Predicting Cancer Neoepitopes

Anna Lisa Schaap-Johansen, Paolo Marcatili

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review


Mutant Peptide eXtractor and Informer (MuPeXI), by Bjerregaard et al. (Cancer Immunol Immunother CII 66:1123-1130, 2017), is a program which identifies tumor-specific peptides and assesses their potential to be neoepitopes. MuPeXI takes as input a VCF file and a list of human leukocyte antigen (HLA) types and optionally a gene expression profile to assess a peptide's potential to be a neoepitope. MuPeXI can be downloaded and run both locally and on a web server. Here, we describe a pipeline for processing the input data so that it can be used for MuPeXI and how to run MuPeXI both locally and as a web server.

Original languageEnglish
Title of host publicationComputer-Aided Antibody Design
Publication date2023
ISBN (Print)978-1-0716-2608-5
ISBN (Electronic) 978-1-0716-2609-2
Publication statusPublished - 2023
SeriesMethods in molecular biology (Clifton, N.J.)


  • Immunotherapy
  • Mutation
  • Neoantigens
  • Neoepitopes
  • Prediction
  • Sequencing
  • Variant calling


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