DNAgent

An agent-friendly DNA design and cloning workbench: a desktop app and a CLI on one Rust engine.

Running a typical cloning design task with DNAgent in Claude Code.

DNAgent is an open replacement for the plasmid viewing and cloning work usually done in SnapGene, built so that a person at the desktop and an AI agent in a terminal work on the same constructs with the same engine.

Research software from the Hochegger Lab. It predicts sequences and products; it does not validate experiments. Check designs before ordering.

Start here

• Installing — macOS and Windows, and how to connect an agent.
• Agent handoff — how the desktop app and an agent share work.
• Restriction sites — the first biological operation, and the model the rest of the engine follows.
• Gibson cloning — the full insert-into-vector workflow.

How to read these pages

Each one is a contract, not a tutorial: what the command does, what it refuses to do, how its output is validated and against what. Where a page says a result is checked against Biopython, the NCBI genetic codes or a brute-force scan, that check runs in CI.

Two conventions hold everywhere:

• Coordinates are zero-based and half-open; end < start wraps through the origin on a circular molecule.
• Source files are never modified in place. Saving always writes a new path, losslessly for everything DNAgent models, or it reports what it could not keep.

The repository README covers installation and the command list; the API documentation is generated from the Rust crates.