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

tf-binding-rs 0.1.4