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.
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. [Epub ahead of print]
PubMed ID: 28429069
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
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.
MuPeXI is available on GitHub.