CloneWay - Molecular Biology Suite

An open-source, GUI-first molecular biology suite for sequence design, analysis, and cloning planning. All data stays in your browser — no accounts, no telemetry, no uploads.

Try CloneWay Online

Features

Sequence Visualization

• Circular Map — SVG plasmid map with feature arcs (wraparound-aware), ORF arcs, restriction site tick marks, de-overlapped labels, selection arc, hover position tooltip, SVG/PNG export
• Linear Map — SVG linear map with adaptive ruler, forward/reverse feature tracks, ORF blocks, staggered restriction cut markers (blunt/5'/3' differentiated), magnifying lens on hover, Ctrl+scroll zoom, SVG/PNG export
• Sequence View — Monospace per-base view with feature coloring, ORF underlines, restriction site bracketing with graph-coloring (8 colors), cut markers, enzyme name labels, protein translation row (for CDS/ORF regions), full keyboard edit mode, Ctrl+scroll zoom

File I/O

• Import: GenBank (.gb, .gbk), FASTA (.fa, .fasta), FASTQ (.fq, .fastq), SnapGene (.dna), AB1 chromatograms (.ab1)
• Export: GenBank (with full wraparound feature support), FASTA
• Drag & drop file import
• Addgene integration — fetch any public plasmid by ID

Sequence Editing

• Edit Mode — type A/T/G/C/N directly into the sequence, backspace/delete to remove, arrow keys to navigate, paste support
• Undo/Redo — 100-step history via temporal middleware (Ctrl+Z / Ctrl+Shift+Z)
• Find — Ctrl+F sequence search with multi-match navigation and IUPAC base filtering

Analysis Tools

• Restriction Site Analysis — 20 common enzymes + 5 Type IIS enzymes (BsaI, BpiI, BbsI, SapI, BsmBI), IUPAC ambiguity support, unique cutter detection
• In-Silico Digest — linear and circular digests with feature coordinate inheritance and overhang calculation
• Gel Visualization — animated SVG electrophoresis with 1kb ladder, log-scale migration, hover details, PNG export
• ORF Finding — all 6 reading frames with configurable minimum length
• Sequence Alignment — Needleman-Wunsch global alignment with affine gap penalties
• BLAST — submit sequences to NCBI BLAST and poll results, via server-side proxy
• Auto-Annotation — exact and approximate matching against a curated database of 50+ known features (promoters, terminators, resistance genes, origins, reporters, tags, recombination sites)
• Chromatogram Viewer — full ABIF (.ab1) chromatogram display with base calls, quality scores, and trace visualization

Cloning Planning

• Restriction/Ligation — plan restriction enzyme digests and ligations
• Gibson Assembly — design overlapping fragments for Gibson assembly
• Golden Gate Assembly — plan Type IIS enzyme-based assemblies
• Site-Directed Mutagenesis — design mutagenesis primers with Wallace-rule Tm calculation

Codon Tools

• Standard codon table with codon usage tables for 5 organisms (E. coli, S. cerevisiae, H. sapiens, C. elegans, D. melanogaster)
• Codon optimization, CAI calculation, protein translation

Project Management

• File System Access API — open, create, save, and load project directories (Chrome/Edge)
• Multi-tab editor with split-pane support
• Feature Library — save, browse, and search reusable features (persisted to localStorage and project directory)
• Recent Sequences — quick access to recently opened sequences

Command Palette (Magic Bar)

• Cmd+K to open — 24 commands across Navigation, Sequence Tools, and File groups
• Keyboard shortcuts for all common actions

Getting Started

npm install
npm run dev

Open http://localhost:3000 in your browser.

Tech Stack

• Framework: Next.js 16 (App Router) + React 19 + TypeScript
• Styling: Tailwind CSS v4 + Framer Motion
• State: Zustand 5 + Zundo (temporal undo/redo)
• UI: Radix UI primitives + cmdk command palette
• Fonts: Inter (UI) + JetBrains Mono (sequence)

Privacy

• All sequence data is stored locally in your browser (localStorage / IndexedDB)
• The Addgene proxy (/api/addgene) fetches public plasmid files — your data is never uploaded
• The BLAST proxy (/api/blast) submits only the query sequence to NCBI
• No analytics, no tracking, no telemetry

License

This project is licensed under the MIT License - see the license.md file for details.

Citation

If you use CloneWay in your research, please cite:

Bruni-Cardoso A., 2026. CloneWay - An open-source, GUI-first molecular biology suite for sequence design, analysis, and cloning planning. https://doi.org/10.5281/zenodo.18851838