oxagorn 0.1.0

Python bindings for Oxagorn - fast tRNA/tmRNA gene finder (PyARAGORN compatible)

Oxagorn

A high-performance Rust reimplementation of ARAGORN for tRNA and tmRNA gene detection.

Why Oxagorn?

ARAGORN (Laslett & Canback, 2004) is a widely-used and well-established tool for detecting tRNA and tmRNA genes in nucleotide sequences. It has become an essential dependency for bacterial genome annotation pipelines such as Bakta, Prokka, and others.

However, ARAGORN was written in C over 20 years ago and has some limitations in modern computing environments:

• Single-threaded only - Cannot utilize multiple CPU cores
• No Python bindings - Requires subprocess calls or external wrappers
• Legacy codebase - Difficult to maintain and extend

Oxagorn addresses these limitations:

• Multi-core support - Parallel processing for 5-6x faster analysis
• Native Python bindings - Drop-in replacement for PyARAGORN
• Modern Rust implementation - Memory-safe, maintainable codebase
• 100% compatible - Identical output to ARAGORN v1.2.41

Performance

Benchmarked on Arabidopsis thaliana genome (120 Mb):

Tool	Time	Speedup
ARAGORN v1.2.41 (C)	26.08s	1.0x
Oxagorn (single-threaded)	24.21s	1.08x
Oxagorn (6 threads)	4.58s	5.7x

Installation

Binary (Rust)

# From source
git clone https://github.com/necoli1822/oxagorn.git
cd oxagorn
cargo build --release

# The binary will be at target/release/oxagorn

Python Package

# From PyPI (coming soon)
pip install oxagorn

# From source
pip install -e .

Note: The Python package requires the oxagorn binary. Set OXAGORN_BIN environment variable or ensure it's in your PATH.

Usage

Command Line (ARAGORN compatible)

# Same options as ARAGORN
oxagorn -t -m -gc11 -w genome.fasta

# With parallel processing (new feature)
oxagorn -@4 genome.fasta  # Use 4 threads

Python (PyARAGORN compatible)

import oxagorn

# Create finder with bacterial genetic code
finder = oxagorn.RNAFinder(translation_table=11)

# Find RNA genes
genes = finder.find_rna(sequence)

for gene in genes:
    if gene.type == "tRNA":
        print(f"tRNA-{gene.amino_acid}({gene.anticodon}) at {gene.begin}-{gene.end}")
    elif gene.type == "tmRNA":
        print(f"tmRNA at {gene.begin}-{gene.end}, tag peptide: {gene.peptide()}")

Bakta Integration

Oxagorn can be used as a drop-in replacement for ARAGORN in Bakta:

# Option 1: Symlink
ln -sf /path/to/oxagorn ~/.local/bin/aragorn

# Option 2: PATH priority
export PATH="/path/to/oxagorn:$PATH"

API Reference

Python Classes

RNAFinder:

RNAFinder(
    translation_table: int = 1,  # NCBI genetic code (1-25)
    trna: bool = True,           # Search for tRNA genes
    tmrna: bool = True,          # Search for tmRNA genes
    linear: bool = False,        # Linear topology (default: circular)
)

TRNAGene: type, begin, end, strand, length, amino_acid, anticodon, sequence()

TMRNAGene: type, begin, end, strand, length, permuted, peptide(), sequence()

License

GPL-3.0 (same as ARAGORN)

Citation

If you use Oxagorn, please cite the original ARAGORN paper:

Laslett, D. and Canback, B. (2004) ARAGORN, a program for the detection of transfer RNA and transfer-messenger RNA genes in nucleotide sequences. Nucleic Acids Research, 32:11-16.

Authors

• Dean Laslett - Original ARAGORN algorithm and implementation
• Sunju Kim (@necoli1822) - Rust reimplementation