readme.md

TF Binding Analysis Tools

This workspace contains tools for analyzing transcription factor (TF) binding sites in DNA sequences:

• tf-binding-rs: A Rust library for TF binding site prediction and sequence analysis
• motif-scanner: A command-line tool for scanning DNA sequences for TF binding sites

🧬 tf-binding-rs

A Rust library providing efficient implementations for:

• FASTA file manipulation and sequence processing
• Position Weight Matrix (PWM) handling
• Energy Weight Matrix (EWM) conversion
• TF binding site occupancy prediction
• Multi-TF occupancy analysis

use tf_binding_rs::occupancy;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let ewms = occupancy::read_pwm_to_ewm("motifs.meme")?;
    let sequence = "ATCGATCGTAGCTACGT";
    let landscape = occupancy::total_landscape(sequence, &ewms, -3.0)?;
    println!("Binding landscape:\n{}", landscape);
    Ok(())
}

🔍 motif-scanner

A command-line tool for scanning DNA sequences and predicting TF binding sites. Features:

• Batch processing of sequence files
• Occupancy score calculation
• Multiple output formats (CSV, Parquet)
• Filtering by occupancy threshold

motif-scanner input.csv motifs.meme output.csv --cutoff 0.2 --mu 9.0

Installation

From Source

# Clone the repository
git clone https://github.com/peter6866/tf-binding-rs
cd tf-binding-rs

# Build both the library and the scanner
cargo build --release --workspace

# Install the motif-scanner binary
cargo install --path motif-scanner

From crates.io

# Install just the motif-scanner tool
cargo install motif-scanner

# For library usage, add to your Cargo.toml:
[dependencies]
tf-binding-rs = "0.1.4"

Documentation

• tf-binding-rs API Documentation
• motif-scanner Usage Guide