MAJIQ-SPEL

MAJIQ-SPEL analyzes local splicing variations (LSVs) from RNA-Seq data to visualize and quantify complex alternative splicing (AS) events and to suggest RT-PCR primers for experimental validation and interpretation of transcript isoforms and affected protein domains.

Key Features:

• Input Handling: Accepts local splicing variations (LSVs) quantified from RNA-Seq datasets as input.
• Visualization and Quantification: Visualizes and quantifies gene isoforms associated with input LSVs, supporting both classical binary splicing events and complex non-binary variations.
• Primer Design Algorithm: Implements a matching primer design algorithm that suggests potential primers for RT-PCR experimental validation.
• UCSC Genome Browser Integration: Displays suggested primers and the corresponding protein domains affected by LSVs on the UCSC Genome Browser.

Scientific Applications:

• Gene Expression Regulation: Enables analysis of how alternative splicing contributes to regulation of gene expression.
• Phenotypic Diversity and Disease Mechanisms: Facilitates investigation of AS contributions to phenotypic diversity and disease mechanisms and identification of potential therapeutic targets.
• High-Resolution Transcriptomic Analysis and Validation: Supports high-resolution analysis of complex splicing events and guides experimental RT-PCR validation of predicted isoforms.

Methodology:

Quantifies local splicing variations from RNA-Seq datasets, processes these LSVs to visualize and quantify associated gene isoforms for binary and non-binary splicing patterns, applies a primer design algorithm to suggest RT-PCR primers, and outputs suggested primers and affected protein domains for display on the UCSC Genome Browser.