io.github.genmnz/jean

up checked 2026-11-11T06:37:56.916Z

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Publisher-provided title

Jean — Molecular Biology & Genomics

Publisher-provided description

Validated molecular biology tools: cloning, primers, CRISPR, Sanger, alignment, qPCR, phylogenetics

Summary by lookupd

Runs molecular biology analyses: cloning, primer design, restriction digests, sequence alignment, read QC, and ENA/GenBank submission prep.

Install

Claude Code, remote (streamable-http)

claude mcp add --transport http jean https://jeanslabs.vercel.app/mcp

Codex, remote (streamable-http)

codex mcp add jean --url https://jeanslabs.vercel.app/mcp

Cursor, remote (streamable-http) → .cursor/mcp.json

{
  "mcpServers": {
    "jean": {
      "url": "https://jeanslabs.vercel.app/mcp"
    }
  }
}

Other clients: docs. Or tell your agent: Set up lookupd for me: read https://lookupd.com/agent.md and follow it.

Tools (showing 30 of 325)

Publisher-provided text

• list_workflow_templates The built-in starter workflows — id, name, what each does and which tools it chains. Pass an `id` to get that template’s graph back, ready to hand to `run_workf
• validate_workflow Would this workflow graph run? Returns the blocking errors — an unknown tool, a wire into a port that does not exist, a cycle — each naming the node and the por
• run_workflow Run a workflow graph: nodes naming tools, wires carrying one node’s output into another’s input, `$whenExpression` to make a step conditional, and `scatter` to
• read_answer_window Read one window of an answer that came back cut to the size budget: the tool, the same arguments, the field its notice named, and which items or characters to r
• describe_tools The full description of each named tool: what it computes, its models and options, and what it refuses. The listing on this endpoint carries only each descripti
• get_open_record Return the plasmid/sequence currently open in the editor. Emits it as a `record`, so it is the SOURCE node of a pipeline — wire its record into any downstream n
• load_record Read a CHOSEN project document as a record — the pipeline's data-reader source, for running on a specific file instead of whatever happens to be open in the edi
• list_library List the project's sequence documents (id, name, length, topology, kind).
• find_restriction_sites Cut positions of the given enzymes on the open plasmid (top/bottom cut, overhang, kind).
• find_star_sites Where the given enzymes could ALSO cut the open plasmid under non-standard conditions, from REBASE's own star-activity list and its one-base rule.
• check_methylation_block Whether the host's own methylation blocks the given enzymes ON THIS PLASMID, from REBASE's methylation-sensitivity tables localised onto your sites.
• digest_reaction_conditions The reaction a digest needs, from NEB's own data: the NEBuffer that serves every enzyme together (scored on the WORST enzyme's percent activity, a star-activity
• enzyme_cut_counts Per-enzyme cut counts on the open plasmid (the EcoRI² superscript-badge numbers).
• export_map_svg Render the open record's map to a publication SVG string, circular or linear — the same figure the Export panel draws, with the same knobs and the same defaults
• run_gel_lane Resolve a gel lane (ladder / plasmid / digest / pcr) into [bp, form] bands for the open plasmid.
• draw_gel Run an agarose gel and photograph it: every lane's fragments migrated by the validated pydna model, drawn as a gel-doc image with the marker ladder's bp marks a
• primer_check Where a primer anneals on the open plasmid: 3'-anchored sites with identity % and the ✓/⚠/~/✗ verdict, graded at a bar you can move and that the answer states.
• design_oligo_plate_order Lay a set of oligos out as a supplier's PLATE order sheet: one worksheet per plate, in the well order the supplier's own order form fills, with the column shape
• build_genbank_submission Turn a record into the SUBMISSION SET NCBI's `table2asn` consumes: a `.fsa` whose defline carries the source modifiers, and a 5-column feature table (`.tbl`) be
• build_ena_submission Turn a record into what ENA's Webin-CLI takes for an annotated sequence (`-context sequence`): an ENA flat file (`.embl`) and its manifest.
• screen_oligo_structure Fold a set of oligos and check them against each other: every oligo's hairpin, its self-dimer anywhere and its self-dimer at the 3' end, plus the cross-dimer wi
• check_manufacturability Measure a sequence against what a NAMED synthesis vendor publishes it can make: length, average and windowed GC, homopolymer runs, tandem repeats, long repeats
• design_gene_fragment_order Write the sheet IDT's gene-fragment PLATE upload takes for one or more designed fragments: one worksheet per 96-well plate, wells in the template's own order, a
• classify_grammar_part Which Golden Braid / MoClo / Yeast ToolKit grammar, position and level the open plasmid represents (or null).
• align_read Pairwise-align ONE sequencing read against a reference and hand on the two gapped rows, so the read can be graded.
• trim_reads Trim sequencing adapters and low-quality ends off FASTQ reads before mapping, and report what was removed.
• fastq_qc FastQC's report on FASTQ reads, every module a default FastQC run reports: per-base quality boxes, per-tile quality (when the headers carry a tile), per-sequenc
• map_reads Map sequencing reads (FASTQ or FASTA) or assembled contigs onto a reference and return the alignment as SAM, the file a pileup viewer, a variant caller or `samt
• verify_read Grade a sequencing read against a reference (✓ verified / ⚠ near / ~ partial / ✗ divergent) from an alignment.
• read_sequencing_qc Read the QC files a sequencing provider returns alongside the reads: a per-base COVERAGE table, or a Plasmidsaurus summary (k-mer composition and the contaminat

Details

• Version: 2.0.0
• Transports: streamable-http
• Uptime (7 days): 100%
• Median latency: 1964 ms
• First indexed: 2026-11-01T09:30:35.371Z
• Last seen in registry: 2026-11-05T14:17:39.204Z
• Website: https://jeanslabs.vercel.app/docs/api/mcp

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