tf-binding-rs (In Development)

A Rust library for predicting transcription factor (TF) binding site occupancy in DNA sequences. This toolkit provides efficient implementations for:

• FASTA file manipulation and sequence processing
• Position Weight Matrix (PWM) handling and Energy Weight Matrix (EWM) conversion
• TF binding site occupancy prediction using statistical thermodynamics
• Binding energy landscape and occupancy probability calculations
• Multi-TF occupancy analysis

Features

• 🧬 Fast FASTA file reading and writing
• 📊 PWM/EWM-based binding site analysis
• 🔍 Efficient sequence scanning with energy matrices
• 📈 Occupancy landscape calculation for multiple TFs
• 🧮 Statistical thermodynamics-based predictions

Installation

Add this to your Cargo.toml:

[dependencies]
tf-binding-rs = "0.1.1"

Or install using cargo:

cargo add tf-binding-rs

Examples

Reading FASTA Files

use tf_binding_rs::fasta;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    // Read sequences from a FASTA file
    let sequences = fasta::read_fasta("path/to/sequences.fasta")?;

    // Print sequence information
    println!("Number of sequences: {}", sequences.height());

    // Calculate GC content
    let gc_stats = fasta::gc_content(&sequences)?;
    println!("GC content analysis: {:?}", gc_stats);

    Ok(())
}

Working with PWM Files

use tf_binding_rs::occupancy;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    // Read PWM motifs from MEME format file
    let pwm_collection = occupancy::read_pwm_files("path/to/motifs.meme")?;

    // Process each motif
    for (motif_id, pwm) in pwm_collection {
        println!("Processing motif: {}", motif_id);
        println!("Matrix dimensions: {:?}", pwm.shape());
    }

    Ok(())
}

Working with PWMs and Energy Matrices

use tf_binding_rs::occupancy;

fn main() -> Result<(), Box<dyn std::error::Error>> {
    // Read PWMs and convert to Energy Weight Matrices
    let ewm_collection = occupancy::read_pwm_to_ewm("path/to/motifs.meme")?;

    // Calculate binding landscape for a sequence
    let sequence = "ATCGATCGTAGCTACGT";
    let mu = -3.0; // chemical potential

    // Get occupancy predictions for all TFs
    let occupancy_landscape = occupancy::total_landscape(
        &sequence,
        &ewm_collection,
        mu
    )?;

    println!("Occupancy predictions:\n{}", occupancy_landscape);
    Ok(())
}

Use Cases

• Genomic sequence analysis
• TF binding site prediction and quantification
• Multi-factor binding landscape analysis
• Regulatory sequence characterization
• Statistical thermodynamics of protein-DNA interactions

Documentation

For detailed API documentation, visit docs.rs/tf-binding-rs