AcrFinder

AcrFinder identifies Anti-CRISPR (Acr) proteins and Acr-Aca operons in genomic sequences to discover and annotate Acrs encoded by prophages that modulate CRISPR-Cas systems despite low sequence similarity and lack of conserved domains.

Key Features:

• Comprehensive mining approach: Integrates homology search, guilt-by-association (GBA), and CRISPR-Cas self-targeting spacer analysis to pre-screen genomic data for potential Acr candidates.
• Acr-Aca operon detection: Mines genomes specifically for Acr-Aca (Anti-CRISPR-associated regulator) operons to identify genomic contexts of Acrs.
• Acr and Aca protein database: Provides a comprehensive database of Acr and Aca proteins enriched through GBA-derived datasets for candidate comparison and annotation.
• Combined methodological framework: Applies homology-based, GBA-based, and self-targeting approaches within a unified analytical workflow to improve discovery of novel Acrs.
• Validation metrics: Demonstrated 100% recall on experimentally characterized datasets using leave-one-out cross-validation.

Scientific Applications:

• Discovery of novel Anti-CRISPR proteins: Enables identification of previously uncharacterized Acrs for experimental validation.
• Annotation of Acr-Aca operons: Supports genomic annotation of Acr-associated regulatory operons in prophage contexts.
• CRISPR-Cas system research: Facilitates studies of CRISPR-Cas regulation and modulation by Acrs.
• Phage–host interaction studies: Contributes to understanding microbial defense mechanisms against phage infections.
• Genome editing research: Informs development and control of CRISPR-based genome editing by identifying Acrs that modulate Cas activity.

Methodology:

Performs homology searches, guilt-by-association (GBA) analyses, and CRISPR-Cas self-targeting spacer analysis to pre-screen genomic data for Acr candidates and evaluates predictions using leave-one-out cross-validation on experimentally characterized datasets.