ornament

Modification-aware tRNA scanner written in Rust.

Ornament identifies tRNAs in genomic sequences using Infernal covariance models, then analyzes sequence compatibility with known RNA modifications to flag "odd" tRNAs that have mutations incompatible with expected modifications.

Features

• tRNA scanning via Infernal covariance models (FFI bindings to libinfernal)
• Modification database with 12+ tRNA modifications from MODOMICS
• Sprinzl position mapping (standard tRNA numbering 1-76)
• Compatibility analysis to detect modification-incompatible variants
• modkit integration for comparing with Nanopore modification calls

Installation

Prerequisites

• Rust 1.70+ (with cargo)
• C compiler (gcc or clang)
• autoconf

Setup

1. Clone the repository:

git clone https://github.com/jayhesselberth/ornament.git
cd ornament

2. Set up dependencies (clones Infernal, HMMER, and Easel):

./scripts/setup-deps.sh

3. Build:

cargo build --release

The binary will be at target/release/ornament.

Usage

Show modification database

# List all modifications
ornament mods

# Show modifications expected at a specific position
ornament mods --position 34 --verbose

# Example output:
# Modifications expected at position 34:
#   inosine (I) - IsotypeSpecific conservation
#   queuosine (Q) - IsotypeSpecific conservation

Scan sequences for tRNAs

ornament scan --input genome.fa --cm tRNA.cm --output results.json

Analyze modification compatibility

ornament analyze --input trnas.json --threshold 0.8

Compare with modkit calls

ornament compare --trna results.json --modkit mods.bedmethyl

Project Structure

ornament/
├── Cargo.toml                 # Workspace manifest
├── scripts/
│   └── setup-deps.sh          # Dependency setup script
├── ext/                       # External deps (gitignored)
│   └── infernal/              # Infernal with hmmer/ and easel/
├── crates/
│   ├── infernal-sys/          # FFI bindings to Infernal/HMMER/Easel
│   │   ├── build.rs           # Compiles C libraries, generates bindings
│   │   └── src/lib.rs
│   ├── ornament-core/         # Core library
│   │   └── src/
│   │       ├── modification/  # Modification types and database
│   │       ├── analysis/      # Compatibility analysis
│   │       ├── infernal/      # Infernal interface
│   │       ├── integration/   # modkit integration
│   │       └── output/        # Output formatters
│   └── ornament-cli/          # CLI binary
│       └── src/main.rs
└── data/                      # Data files

Modification Database

The database includes common eukaryotic tRNA modifications:

How It Works

1. Scan: Use Infernal cmsearch to find tRNAs in input sequences
2. Map: Align hits to Sprinzl tRNA positions (1-76)
3. Analyze: Check each position for modification compatibility
   • If a position expects modification X (derived from base Y)
   • But the sequence has base Z (incompatible with X)
   • Flag as "odd" tRNA
4. Report: Output compatibility scores and incompatibilities

Development

# Run tests
cargo test

# Build in debug mode
cargo build

# Run clippy
cargo clippy

# Format code
cargo fmt

License

MIT

References

• Infernal - RNA covariance model search
• MODOMICS - RNA modification database
• tRNAscan-SE - tRNA detection
• modkit - Nanopore modification toolkit