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 biophysical models
Information content and binding site diversity calculations

Built with performance in mind, this library offers a fast and memory-efficient alternative to traditional Python implementations for genomic analysis.

Features

🧬 Fast FASTA file reading and writing
📊 PWM/EWM-based binding site scoring
🔍 Efficient sequence scanning for binding sites
📈 Occupancy landscape calculation
🧮 Statistical and thermodynamic calculations

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(())
}

Use Cases

Genomic sequence analysis
TF binding site prediction
Regulatory sequence characterization
High-throughput DNA sequence processing

Documentation

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

tf-binding-rs 0.1.3