LibreGene — Plasmid Editor

中文版

A lightweight cross-platform desktop plasmid editor. Feature annotation, primer design, restriction analysis, sequence alignment, RNA folding — all free and open-source.

Features

Feature Annotation

• Clean, minimal display — CDS and mRNA features are translated on the fly, amino acids rendered right under the sequence
• Auto-detection — paste a sequence into the New Sequence dialog and common features (promoters, resistance markers, ori, tags…) are detected automatically and can be annotated with one click
• ORF search — scan open reading frames on both strands, all six frames, displayed inline
• GC content track — sliding-window GC% rendered as a gradient band below the sequence, with adjustable window size
• Compound (multi-segment) features, custom colors, strand toggling, enriched GenBank I/O that preserves colors and primers

Primers

• Binding visualization — mismatches, annealing region and Tm shown at a glance for every primer
• Assisted design — fragment amplification, overlap-extension PCR (OE-PCR) and site-directed mutagenesis, with candidates ranked by Tm / GC% and optional restriction-site tails

Codon Optimization

• 9 species codon usage tables — optimize any CDS/mRNA feature for the expression host of your choice
• Three strategies — use best codon, match codon usage, or harmonize against the source species
• Preview before applying — translation check, CAI and GC% before/after at a glance; optionally avoid creating specified restriction sites

Restriction Enzymes

• Built-in 900+ enzyme database with methylation-aware filtering
• Clear categorization — unique cutters, twice cutters, blunt ends and Type IIS enzymes are distinguished visually, and cut sites are marked on the feature scrollbar for quick navigation
• Custom enzyme sets — define your own enzyme collections and switch between them
• Provider detail data — per-enzyme buffer compatibility, incubation temperature, methylation sensitivity and inactivation info from New England Biolabs, Thermo Fisher FastDigest and Yugong Biotech (BestEnzymes)

Digest and Run Gel

• In-silico digest simulation — pick enzymes, set cutting efficiency, and enumerate every resulting fragment, including partial-digest products
• Virtual gel electrophoresis — agarose/PAGE matrix, concentration and run-time controls with built-in or custom ladders; topology-aware migration (uncut circles run as supercoiled bands) and band diffusion are modeled

Sequence Alignment

• Multiple formats — import Sanger reads (.ab1), FASTA or GenBank sequences and align them against the reference
• Mismatches, insertions and deletions highlighted in place, per-read identity computed automatically
• Sanger chromatogram display — open a .ab1 file to see its trace curves alongside the sequence

RNA Secondary Structure

• MFE folding — minimum-free-energy secondary structure prediction, computed locally
• Interactive layout — force-directed structure view with pan/zoom and draggable nucleotides; can be shown as the editor background

MCP / LLM Agent Integration

LibreGene embeds an MCP server (loopback only at 127.0.0.1:8766, Bearer-token auth) so an LLM agent in your terminal can operate the open plasmid like a real user — while the UI updates live. Launch LibreGene, open the MCP Server dialog in the sidebar (or the "Connect an LLM agent via MCP" link on the empty screen), and copy the auto-generated setup prompt — with the URL and access token embedded — to your agent; it configures the connection itself.

16 tools are exposed, covering the full editing workflow:

• Projects & files — open_project, save_file (with subsequence/region export), list_workspace, add_to_workspace
• Reading — read_sequence, get_project_overview, get_region_view
• Editing — edit_sequence (insert/delete/replace), set_feature (create & update)
• Primers — add_primer, test_primers (ad-hoc binding checks with Tm and amplicon size), design_primers (amplify / OE-PCR / mutagenesis)
• Analysis — find_restriction_sites, find_orfs, add_alignment, convert_sequence (sequence conversion + codon optimization for 9 species)

Example Tasks

Ready-to-run agent tasks live in examples/tasks, each with a Prompt.txt you can hand to your agent and a reference result:

• Primer Design — clone mEGFP into a BamHI/HindIII-digested BlueScribe vector: design cloning primers with restriction tails, pick colony-PCR verification primers, then design A206K mutagenesis primers
• Alignment — given pVA-MCS and three Sanger .ab1 reads, determine which samples successfully mutated away the BbsI site
• RNAi — given a vector and an experimental protocol, design an RNAi plasmid targeting a gene of interest with a given antisense sequence
• CAR-T — given the amino-acid sequence of an anti-CD19 CAR (FMC63 scFv–CD28–CD3ζ), design a pLVX-CAR-IRES-ZsGreen1 expression vector

And More

• Circular plasmid map view alongside the sequence editor
• DNA / RNA / protein modes — single-strand editors for RNA and protein sequences
• Wrap and continuous view modes — multi-line wrapping or a single horizontally scrollable line
• BLAST search — right-click any selection to submit it to NCBI BLAST
• SnapGene history — browse snapshots embedded in .dna files
• Plugin system — extensible architecture for adding custom tools
• Multi-project tabs — switch between plasmids in the sidebar
• Full undo/redo — sequence edits and feature changes
• GenBank / SnapGene / FASTA I/O — read/write .gb/.gbk and protein .gpt; read .dna/.rna/.prot (SnapGene), FASTA and Sanger .ab1

Plugins

LibreGene supports plugins — the dotplot viewer and gel simulator in src/plugins/ are examples. Want to build one? Check the plugin development guide and open a PR. Contributions welcome!

Installation

macOS (Homebrew, Apple Silicon):

brew install --cask dl-li/libregene/libregene

The app is not notarized yet, so on first launch use right-click → Open (or approve it in System Settings → Privacy & Security).

Alternatively, download installers for macOS (dmg), Windows (msi / nsis) and Linux (Flatpak) directly from GitHub Releases.

Quick Start

npm install
npx tauri dev

Requires Node.js ≥ 20, Rust ≥ 1.75, and Tauri v2 prerequisites.

License

GNU General Public License v3.0 — see LICENSE.

Copyright (C) 2025 dl-li

Acknowledgements

Thanks to our contributors liu1568075 and Masterchiefm.

This project also builds on many great open-source tools, including pLannotate, pydna, DNA Chisel, Biopython and RibossFold.