Book chapter ยท Journal article
A Computational Pipeline for Predicting Cancer Neoepitopes
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.
Language: | English |
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Publisher: | Springer US |
Year: | 2023 |
Pages: | 475-488 |
Series: | Methods in Molecular Biology (clifton, N.j.) |
ISBN: | 1071626086 , 1071626094 , 9781071626085 and 9781071626092 |
ISSN: | 10643745 and 19406029 |
Types: | Book chapter and Journal article |
DOI: | 10.1007/978-1-0716-2609-2_27 |
ORCIDs: | Marcatili, Paolo |
Immunotherapy Mutation Neoantigens Neoepitopes Prediction SDG 3 - Good Health and Well-being Sequencing Variant calling