Project - High-performance gene prediction & genome annotation in Rust
Orphos is a modern Rust-based implementation of a prokaryotic gene finding algorithm that identifies protein-coding genes in microbial genomes. It applies an unsupervised machine-learning dynamic programming approach to genome annotation and supports both single genomes and metagenomic data.
- Name
- Orphos
- Year
- Category
- Open Source · Bioinformatics
Overview
Orphos is an open-source genome annotation tool focused on prokaryotic gene prediction — the task of identifying protein-coding genes in bacterial and archaeal genomes. At its core, Orphos implements a dynamic programming gene-finding algorithm originally used in tools like Prodigal, rewritten in Rust to emphasize performance, safety, and maintainability. 
Traditional gene prediction tools were often written in older languages such as C, making them challenging to maintain, extend, or integrate into modern workflows. Orphos leverages Rust’s memory safety, strong type system, and parallelism facilities to provide a fast and robust alternative that can be used in both research and applied bioinformatics settings. 
Beyond the core annotation engine, Orphos offers a command-line interface and library API, with optional Python bindings — allowing integration into data science environments, workflows, or pipelines without resorting to fragile script chaining.
Features
- Rust implementation
- Python bindings
- WebAssembly bindings
- Original Prodigal
- ~4.2s
- Orphos single-threaded
- ~3.24s
- Orphos with 8 threads
- ~2.70s