A new publication from our lab on Software Impact describes the current version of JCAST (v.0.3.3). JCAST is a Python tool to perform in silico translation of alternative splicing transcripts into custom protein sequences. JCAST takes in RNA sequencing data processed by an upstream STAR/rMATS workflow and produces protein sequence databases in FASTA formats that can be used in bottom-up proteomics database search workflows. Splice junctions in the cell are thought to follow a bimodal distribution of total junction read counts, with the low abundance junctions thought to be less likely translatable into functional polypeptide chains. The current version of JCAST implements read count modeling using a Gamma/Gaussian mixture model to discard low-abundance splice junctions and limit database size. This software tool has been used to identify alternative splicing derived proteoforms in various human tissues as well as during human induced pluripotent stem cell differentiation.
See here for the JCAST software description: https://www.sciencedirect.com/science/article/pii/S2665963821000695
A reproducible repository is also given on CodeOcean: https://codeocean.com/capsule/7792521/tree