# Prophage ACR Screening Pipelines

This directory contains two analysis pipelines for screening Anti-CRISPR (Acr) proteins from prophage genomes.

## Directory Structure

| 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 |

## Quick Navigation

- **[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.

## Detailed Documentation

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

Click the links above to view detailed documentation for each pipeline.