Alternative Splicing Analysis Module

Visualize and analyse alternative splicing events.

The Alternative Splicing Analysis module provides comprehensive visualization and analysis of alternative splicing events and their impact on peptide generation.

Supported Splicing Event Types

  • SE – Skipped Exon

  • A3SS – Alternative 3’ Splice Site

  • A5SS – Alternative 5’ Splice Site

  • MXE – Mutually Exclusive Exons

  • RI – Retained Intron

Input Support

  • rMATS – Process and visualize rMATS output files

  • SplAdder – Compatible with SplAdder results

Key Features

  • Interactive visualization of splicing events

  • Peptide consequence mapping

  • Event statistics and quantification

  • Comparison across conditions

  • Export visualizations and data

Workflow

  1. Select the analysis mode (rMATS or SplAdder).

  2. Upload output files and select the splicing event type.

  3. Generate inclusion/exclusion protein isoforms from the selected event.

  4. Configure visualization parameters (enzyme, missed cleavage).

  5. Compare rMATS-derived protein isoforms with known gene transcripts.

  6. View multi-protein-isoform comparative visualization and peptide impacts.

  7. Export results and figures.

rMATS Analysis interface

rMATS Peptide Analysis interface showing the analysis pipeline with rMATS/SplAdder tabs, file upload, event type selection, protein isoform generation, and multi-protein-isoform comparative visualization controls.

Multi-protein-isoform comparative analysis results

Multi-Isoform Comparative Analysis results showing rMATS-derived inclusion/exclusion protein isoforms compared with known gene transcripts, with peptide maps and a highlighted protein isoform peptide table showing specificity classifications.

Output

The module generates:

  • Splicing event diagrams

  • Inclusion/exclusion protein isoform peptide maps

  • Multi-protein-isoform comparative visualizations

  • Peptide specificity tables

  • Exportable visualizations