SeqCraft

SeqCraft is a browser workbench for viewing, editing, and analyzing DNA and RNA. It runs sequence work locally and gives browser agents a safe tool interface through WebMCP.

Open SeqCraft · Technical reference · Security policy

What it does

• Opens FASTA, GenBank, and SeqCraft files.
• Shows linear, circular, and 3D plasmid maps.
• Finds features, primers, restriction sites, and open reading frames.
• Simulates restriction digests, PCR, and Golden Gate assembly.
• Scans CRISPR targets for SpCas9, SaCas9, Cas12a, and Cas12e.
• Compares constructs and keeps undo/redo history.
• Exports FASTA, GenBank, SeqCraft JSON, and Opentrons Python protocols.
• Provides 57 WebMCP tool identifiers for browser agents.

Privacy and control

Raw sequences, annotations, primers, and derived constructs stay in the browser. The optional server stores account details and sequence-free project metadata only.

Agent-proposed sequence changes are staged for review. SeqCraft shows the proposed change and checks its revision before the user can apply it.

WebMCP tool reference

SeqCraft exposes 57 tool identifiers through document.modelContext. Five are compatibility aliases, so they represent 52 distinct operations. The live technical reference adds descriptions, effects, search, and scientific limits.

Show all WebMCP tools

Context

Read what is open, selected, supported, or waiting for approval.

seqcraft_get_capabilities
seqcraft_get_workspace_context
seqcraft_get_selected_context
seqcraft_get_document_revision
seqcraft_get_transaction_status

Workspace

Move between documents and views, or change the visible selection.

seqcraft_set_active_document
seqcraft_set_active_view
seqcraft_select_range
seqcraft_select_feature
seqcraft_clear_selection
seqcraft_focus_region

Documents

List, create, copy, rename, or remove documents.

seqcraft_list_documents
seqcraft_get_active_document
seqcraft_create_document
seqcraft_duplicate_document
seqcraft_update_document_metadata
seqcraft_delete_document

Sequence changes

These stage sequence-changing work for human review.

seqcraft_edit_sequence
seqcraft_reverse_complement_region
seqcraft_rotate_origin
seqcraft_copy_region_between_documents

seqcraft_create_document_from_region creates a new document from a selected region.

Features

Read, find, show, or change annotations.

seqcraft_list_features
seqcraft_show_feature
seqcraft_mutate_feature
seqcraft_detect_known_features
seqcraft_propose_annotation

Primers and PCR

seqcraft_list_primers
seqcraft_mutate_primer
seqcraft_analyze_primer
seqcraft_simulate_pcr

Restriction and cloning

seqcraft_analyze_restriction_sites
seqcraft_show_restriction_site
seqcraft_simulate_digest
seqcraft_simulate_golden_gate
seqcraft_domesticate_sequence
seqcraft_stage_domestication_candidate
seqcraft_prepare_restriction_clone

Analysis

seqcraft_compare_documents
seqcraft_find_orfs
seqcraft_find_crispr_targets
seqcraft_screen_biosecurity

History

seqcraft_get_history
seqcraft_undo
seqcraft_redo
seqcraft_restore_revision

Import, search, and export

seqcraft_import_sequence_text
seqcraft_search_sequence_database
seqcraft_import_from_database
seqcraft_export_document

Automation

seqcraft_generate_opentrons_protocol
seqcraft_execute_actions

Compatibility aliases

Alias	Same operation as
seqcraft_get_pending_transaction	seqcraft_get_transaction_status
seqcraft_select_sequence_range	seqcraft_select_range
seqcraft_plan_domestication	seqcraft_domesticate_sequence
seqcraft_stage_sequence_transaction	seqcraft_stage_domestication_candidate
seqcraft_export_sequence	seqcraft_export_document

Run locally

Requirements: Node.js 20 or newer and npm 10 or newer.

git clone https://github.com/sea-deep/seqcraft.git
cd seqcraft
npm install
npm run dev:all

Open http://localhost:5173. SeqCraft works in guest mode without a database or login setup.

Optional accounts and Google sign-in

Copy .env.example to .env, then set these server values:

MONGODB_URI=your-mongodb-connection-string
BETTER_AUTH_SECRET=at-least-32-random-characters
BETTER_AUTH_URL=http://localhost:8787
APP_ORIGIN=http://localhost:5173

For Google sign-in, also set:

GOOGLE_CLIENT_ID=your-google-client-id
GOOGLE_CLIENT_SECRET=your-google-client-secret

Add this authorized redirect URI in Google Cloud:

http://localhost:8787/api/auth/callback/google

For a deployed backend, replace http://localhost:8787 with its public HTTPS URL. The frontend can point to that backend with the VITE_API_URL build variable.

Check changes

npm test
npm run build

The test suite covers sequence math, circular coordinates, file handling, storage, authentication, WebMCP, and user-interface flows.

Important limits

SeqCraft predicts sequence-level results. It does not replace wet-lab checks for reaction conditions, primer secondary structure, CRISPR off-targets, robot setup, or formal biosecurity review. The technical reference explains each model and its limits.

Project layout

src/          browser application and scientific code
server/       optional authentication and metadata API
test/         unit and integration tests
docs/assets/  screenshots used by this README

License

MIT