Change Log

JCAST software for alternative splicing proteomics analysis. Create custom protein databases using RNA-seq data to identify unique protein alternative splicing isoforms in mass spectrometry experiments
Author

Edward Lau, Maggie Lam

Published

March 1, 2026

Abstract
This page provides the documentation for the JCAST package, which is a tool for create a database of protein isoforms from RNA-seq data.
Keywords

Alternative splicing, proteomics, mass spectrometry, RNA sequencing, protein isoforms, proteoforms

v0.3.5a

  • JCAST will now skip a junction if the nucleotide sequence contains masked bases
  • Added the –mask argument to determine masked nucleotide letters (default: NnXx)
  • Added an option to translate only a subset of splice types (MXE, RI, SE, A3SS, A5SS) with the -s argument

v0.3.5

  • Fixed an issue where a small number of slices were not translated.
  • Fixed an issue where JCAST quits if the model flag is not set.

v0.3.2

  • The -q –qvalue option now works by including splice junctions within the specified range. To preserve the previous behavior, use -q 0.01 1. The default -q 0 1 disables filtering.
  • The -c –canonical argument now defaults to False. To preserve prior behaviors, manually set the -c flag to translate canonical proteins detected in the RNA-seq experiments even if isoform translation failes
  • The -c –canonical argument now will translate a canonical sequence even if a splice event has low skipped junction counts or falls outside of the specified fdr range
  • JCAST now automatically models the likely translatable junction count threshold through the -m –model argument. Previously this was done manually then set as an integer (minimal read count) using the -r –read argument.
  • The skipped junction counts used for modeling now consider the sum of all biological and technical replicates rather than the minimum

v0.3.1

  • Fixed issues where Gencode GTF files without transcript_biotype annotations could not be read
  • Fixed issues of retrieving Uniprot canonical sequences from Ensembl transcript versions
  • Compatibility with biopython>=1.78

v0.2.8

  • Fixed an issue where jcast is called twice from the direct cli entry point
  • Added option to use longest coding sequence from GTF as canonical

v0.2.6

  • Fixed an issue where some A5SS minus-strand transcripts had incorrect phases retrieved from gtf
  • Fixed an issue where some transcripts using a secondary translation start sites are not trimmed