SAPFIR

SAPFIR identifies protein features affected by alternative splicing by mapping InterProScan-predicted domains, motifs, and sites to transcripts in human and mouse to support functional interpretation of isoform diversity.

Key Features:

• Predictive Analysis: Uses InterProScan to analyze protein sequences for functional domains, motifs, and sites and links these predicted features to specific alternative splicing events in human and mouse.
• Data Integration: Integrates transcript data with splice site information to present alternative protein features as functions of transcripts and isoforms.
• Scalability: Processes large sequence datasets and can analyze proteins from a single gene or multiple genes simultaneously for high-throughput studies.
• Validation: Rediscovered previously confirmed alternative protein domains, supporting the accuracy of its predictions.
• Comparative Insights: De novo analysis of public datasets reveals conservation of alternative protein domains between human and mouse and indicates enrichment of domain-losing isoforms in genes involved in nervous system processes, regulation of DNA-templated transcription, and aging.

Scientific Applications:

• Functional interpretation of alternative splicing: Identify which protein domains, motifs, or sites are gained or lost due to alternative splicing to infer potential functional consequences.
• Comparative genomics: Assess conservation of alternative protein domains between human and mouse to prioritize conserved splicing events.
• Biological process and disease studies: Investigate splicing-driven loss of functional domains in research areas such as neurobiology, transcription regulation, and aging.

Methodology:

InterProScan is used to predict domains, motifs, and sites from protein sequences, and these predictions are mapped to transcripts using transcript and splice site information; de novo analyses of public datasets are performed for conservation and enrichment studies.