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INTEGRATE-Neo
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A neoantigen discovery pipeline to identify gene fusions in prostate cancers that may produce neoantigens. INTEGRATE-Neo, is comprised of the following steps: (i) gene fusion peptide prediction, (ii) HLA allele prediction, and (iii) gene fusion neoantigen discovery. To ensure user=friendliness, all of the modules within INTEGRATE-Neo are designed as standalone tools with their own optional parameters. Authors apply INTEGRATE-Neo to the TCGA prostate cohort data to demonstrate its utility for identifying gene fusion neoantigens that may serve as personalized cancer immunotherapy targets.
MuPeXI / Mutant peptide extractor and informer
Identifies tumor-specifc peptides and assess their potential to be neo-epitopes. MuPeXI is based on priority score intended to rank peptides according to likelihood of eliciting a T cell response. It returns tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, enriched with comprehensive annotation, including HLA binding and similarity to normal peptides. The tool allows the user to select the most likely immunogenic peptides.
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