biostudies-literaturePrelot LLOOP ZürichETH core fundingCommon Fund of the Office of the Director of the National Institutes of HealthThe LOOP Zurich and the “Monique Dornonville de la Cour—Stiftung”NHGRININDSNIMHThe LOOP Zurich and the "Monique Dornonville de la Cour-Stiftung"NHLBINCISwiss Molecular Pathology Breakthrough PlatformSwiss Molecular Pathology Breakthrough Platform (SOCIBP)NIDAbtaf492https://www.ebi.ac.uk/biostudies/studies/S-EPMC12777967biostudies-literatureUnknown42(1)<h4>Motivation</h4>RNA sequencing enables the characterization of a cell's transcript isoforms in healthy and disease conditions. In the context of cancer, local transcript variability may translate to splicing-derived tumor-associated peptides recognized by the immune system. A software tool that extracts such candidate peptides, is of great interest for personalized cancer therapy.<h4>Results</h4>We present the open-source software tool ImmunoPepper, which extracts a set of biologically plausible peptides from a splicing graph, derived from a set of RNA-seq datasets. This peptide set can be personalized with germline and somatic variation and takes novel RNA splice variants into account. ImmunoPepper supports several filtering options, including subtraction of normal tissue background, pBioinformatics (Oxford, England)ImmunoPepper: extracting personalized peptides from complex splicing graphs.PMC12777967PHRT106 /SPHN017DRI19Chen JKahles ARatsch GPrelot LHuser MfalseImmunoPepper: extracting personalized peptides from complex splicing graphs.<h4>Motivation</h4>RNA sequencing enables the characterization of a cell's transcript isoforms in healthy and disease conditions. In the context of cancer, local transcript variability may translate to splicing-derived tumor-associated peptides recognized by the immune system. A software tool that extracts such candidate peptides, is of great interest for personalized cancer therapy.<h4>Results</h4>We present the open-source software tool ImmunoPepper, which extracts a set of biologically plausible peptides from a splicing graph, derived from a set of RNA-seq datasets. This peptide set can be personalized with germline and somatic variation and takes novel RNA splice variants into account. ImmunoPepper supports several filtering options, including subtraction of normal tissue background, p2026-01-01T00:00:00Z2026 Jan2026-06-06T11:35:36.112Z2026-05-29T03:13:24.105ZS-EPMC127779674106540810.1093/bioinformatics/btaf492