spliceR

spliceR analyzes alternative splicing events and predicts coding potential and nonsense-mediated decay (NMD) sensitivity from full-length transcript assemblies derived from RNA-seq to detect and annotate transcript isoform changes across experimental conditions.

Key Features:

• Alternative Splicing Classification: Detects single and multiple exon skipping, alternative donor and acceptor site usage, intron retention, alternative first or last exon usage, and mutually exclusive exons, and annotates genomic coordinates of differentially spliced elements.
• Transcript Isoform Analysis: Calculates fraction values per transcript isoform to identify transcript switching between different experimental conditions.
• Coding Potential and NMD Sensitivity Prediction: Predicts the coding potential of each transcript isoform and assesses potential sensitivity to nonsense-mediated decay (NMD).
• Input Data: Operates on full-length transcript outputs generated by RNA-seq assemblers as primary input.

Scientific Applications:

• Post-transcriptional regulation analysis: Enables investigation of gene expression regulation at the post-transcriptional level by characterizing alternative splicing events.
• Genomics and transcriptomics research: Supports studies in genomics, transcriptomics, and molecular biology to explore how alternative splicing contributes to protein diversity and disease mechanisms.
• RNA-seq assembly annotation: Provides deeper annotation of assembled transcripts to facilitate downstream sequence and functional analyses.

Methodology:

Uses full-length transcripts generated by RNA-seq assemblers to identify and annotate alternative splicing events and to predict coding potential and NMD sensitivity for each transcript isoform.