JCAST - Junction Centric Alternative Splicing Translator

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.

Edward Lau, Maggie Lam


October 31, 2022

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


JCAST (Junction Centric Alternative Splicing Translator) is a Python software that takes in splicing events from RNA sequencing data to create custom protein sequence databases for protein isoform analysis.

JCAST attempts to create small protein sequence databases that contain only likely sequences in mass spectrometry experiment samples to avoid runaway database size inflation.

To do so, JCAST likely translatable alternative splice junctions and performs one-frame in silico analysis, then joins the translated variant sequences with full-length canonical sequences.

JCAST Workflow


Latest Updates


  • 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


  • 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.

See Change Log for details.

The latest version and source code of JCAST can be found on github: https://github.com/ed-lau/jcast.

See the Quick Start and Documentation for instructions.



  1. JCAST: Sample-Specific Protein Isoform Databases for Mass Spectrometry-based Proteomics Experiments. RW Ludwig, E Lau Software Impacts 10, 100163 Link

  2. Determining Alternative Protein Isoform Expression Using RNA Sequencing and Mass Spectrometry. Y Han, JM Wright, E Lau, MPY Lam STAR Protocols 1 (3), 100138 Link

  3. Splice-Junction-based Mapping of Alternative Isoforms in the Human Proteome. E Lau, Y Han, DR Williams, CT Thomas, R Shrestha, JC Wu, MPY Lam Cell Reports 29 (11), 3751-3765. e5 Link