| # Prophage ACR Screening Pipelines |
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| This directory contains two analysis pipelines for screening Anti-CRISPR (Acr) proteins from prophage genomes. |
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| ## Directory Structure |
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| | Folder | Description | |
| |--------|-------------| |
| | [double_diff/](double_diff/README.md) | Double-divergence screening pipeline: identifies novel Acr candidates that are **significantly different** from known Acr proteins at both sequence and structure levels | |
| | [double_similar/](double_similar/README.md) | High-confidence Acr identification pipeline: identifies high-confidence Acr candidates that are **highly similar** to known Acr proteins at both sequence and structure levels | |
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| ## Quick Navigation |
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| - **[double_diff](double_diff/README.md)** — For discovery of Acrs with novel mechanisms. Excludes proteins with sequence homology (qcovs≥30, pident≥30) or structural similarity to known Acrs, retaining "double-divergent" candidates. |
| - **[double_similar](double_similar/README.md)** — For expansion of known Acr families. Applies stringent filters for sequence (qcovs≥50, pident>50) and structural (TM-score>0.7, prob=1.0) similarity to obtain high-confidence candidates. |
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| ## Detailed Documentation |
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| Each folder contains a comprehensive README document describing: |
| - Screening strategies and workflows |
| - Input and output data formats |
| - Software tools and parameter settings |
| - Screening thresholds and criteria |
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| Click the links above to view detailed documentation for each pipeline. |
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