A high-performance Rust implementation of the Z-DNA formation prediction algorithm, originally developed by Ping-jung Chou under the instruction of Pui S. Ho.

Z-HUNT-3 is a computational tool that predicts the formation of Z-DNA (left-handed DNA) in naturally occurring sequences using a thermodynamic approach. This implementation is based on the seminal paper "A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences" published in The EMBO Journal, Vol.5, No.10, pp2737-2744, 1986.

• High Performance: Optimized Rust implementation with parallel processing capabilities
• Memory Efficient: Uses dynamic programming to reduce complexity from O(2^n) to O(n)
• Configurable Threading: Support for both parallel and sequential processing
• FASTA Support: Processes DNA sequences in FASTA format
• Statistical Analysis: Provides Z-scores and probability calculations for Z-DNA formation

• Rust 1.70 or later
• Cargo (comes with Rust)

git clone <repository-url>
cd zhunt
cargo build --release

The optimized binary will be available at target/release/zhunt.

zhunt <window_size> <min_size> <max_size> <filename> [OPTIONS]

• window_size: Window size in dinucleotides
• min_size: Minimum size for analysis
• max_size: Maximum size for analysis
• filename: Input sequence file (FASTA format)

• -t, --threads <THREADS>: Number of threads to use (0 = auto-detect) [default: 0]
• -s, --sequential: Use sequential processing instead of parallel
• -h, --help: Print help information
• -V, --version: Print version information

# Basic usage with auto-detected threads
./zhunt 50 6 50 sequence.fasta

# Use specific number of threads
./zhunt 50 6 50 sequence.fasta --threads 8

# Force sequential processing
./zhunt 50 6 50 sequence.fasta --sequential

The program generates a .Z-SCORE file containing:

• Position information (start and end positions)
• Sequence length
• Delta linking number
• Slope values
• Probability scores
• DNA sequence segments
• Anti-syn configuration strings

filename sequence_length min_size max_size
position end_position length delta_linking slope probability sequence antisyn_config

The algorithm uses thermodynamic calculations to predict Z-DNA formation by:

1. Energy Calculation: Computing delta BZ energy for dinucleotide pairs
2. Configuration Analysis: Evaluating anti-syn conformations using dynamic programming
3. Linking Number: Calculating optimal delta linking numbers
4. Statistical Assessment: Providing probability scores based on normal distribution

• Parallel Processing: Uses Rayon for multi-threaded computation
• Memory Layout: Optimized data structures for cache efficiency
• Vectorization: Loop unrolling and SIMD-friendly operations
• Dynamic Programming: Reduces exponential complexity to linear

• clap: Command-line argument parsing
• anyhow: Error handling
• memmap2: Memory-mapped file I/O
• rand: Random number generation
• rayon: Data parallelism

Z-DNA is a left-handed double helix form of DNA that can form under certain conditions, particularly in sequences with alternating purine-pyrimidine patterns. The formation of Z-DNA has biological significance in:

• Gene regulation
• Chromatin structure
• DNA-protein interactions
• Genomic instability

This tool helps researchers identify potential Z-DNA forming regions in genomic sequences, which can be important for understanding regulatory mechanisms and structural biology.

The Rust implementation provides significant performance improvements over the original implementation:

• Multi-threading: Scales with available CPU cores
• Memory Efficiency: Reduced memory footprint through optimized data structures
• Cache Optimization: Improved memory access patterns
• Vectorization: Better utilization of modern CPU features

• FASTA format: Standard nucleotide sequence files
• Supported bases: A, T, G, C, N (case-insensitive)
• Circular sequences: Automatically handles sequence circularity

• Z-SCORE files: Tab-separated values with detailed analysis results
• Progress reporting: Real-time processing status updates

Contributions are welcome! Please ensure that:

1. Code follows Rust best practices
2. Performance optimizations maintain correctness
3. Tests are included for new features
4. Documentation is updated accordingly

This project maintains the spirit of the original research while providing a modern, high-performance implementation.

If you use Z-HUNT-3 in your research, please cite the original paper:

Chou, P.J. and Ho, P.S. (1986) A computer aided thermodynamic approach for predicting the formation of Z-DNA in naturally occurring sequences. The EMBO Journal, 5(10), 2737-2744.

• Original algorithm by Ping-jung Chou and Pui S. Ho
• Rust implementation optimizations and modernization
• Community contributions and feedback