NMD classifier

NMD classifier classifies nonsense-mediated decay (NMD) events by identifying and categorizing transcript structural changes associated with premature termination codons to support studies of gene regulation, transcriptome dynamics, and evolution.

Key Features:

• Minimal evolution/regulation principle: Operates on the principle of minimal evolution or regulation, favoring the transcript structural change that involves the least alteration.
• High accuracy (simulation): Simulation results report approximately 99.3% correct identification of NMD-causing transcript structural changes, notably exon inclusions/exclusions and exon boundary alterations.
• Supports annotated and de novo transcripts: Classifies both annotated transcripts and de novo assembled transcripts.
• Comparative capability: Enables comparison of NMD events across biological conditions or organisms to investigate the evolutionary and regulatory origins of NMD-targeted transcripts (NMDTs).

Scientific Applications:

• Gene regulation studies: Identifies NMD-targeted transcripts and their structural causes to analyze NMD-mediated regulation of gene expression.
• Transcriptome dynamics: Detects structural transcript changes that trigger NMD to study transcriptome composition and dynamics.
• Evolutionary biology: Facilitates cross-species or comparative analyses of NMD events to infer evolutionary origins of NMDTs.
• NMDT characterization: Systematically classifies NMD-targeted transcripts for downstream analyses of function and origin.

Methodology:

Classifies annotated and de novo assembled transcripts by identifying minimal transcript structural changes consistent with nonsense-mediated decay (principle of minimal evolution/regulation) and was validated by simulations reporting ~99.3% correct identification of NMD-causing structural changes, including exon inclusions/exclusions and exon boundary alterations.