SplicingViewer

SplicingViewer analyzes RNA-Seq data to detect, annotate, and visualize alternative splicing events genome-wide.

Key Features:

• Detection of Splice Junctions: Detects splice junctions in RNA-Seq data to identify intron removal and exon–exon boundaries in pre-mRNA and mature mRNA.
• Annotation of Alternative Splicing Events: Annotates and classifies alternative splicing events including exon skipping, intron retention, and mutually exclusive exons.
• Visualization of Splicing Patterns: Generates visualizations of alternative splicing patterns across genes and transcripts.
• Versatile Computational Pipeline: Implements an integrated computational pipeline for in-depth analysis and classification of alternative splicing events and scalable handling of large, high-throughput RNA-Seq datasets.

Scientific Applications:

• Eukaryotic Gene Expression: Characterizing alternative splicing to study regulation of eukaryotic gene expression.
• Protein Isoform Diversity: Investigating how alternative splicing generates protein isoform diversity from a limited number of genes.
• Disease and Systems Biology: Identifying aberrant splicing events relevant to complex biological systems and diseases.

Methodology:

Processes RNA-Seq data through an integrated computational pipeline to detect, annotate, and visualize splice junctions and alternative splicing events.