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# SeqCraft: 57 WebMCP tools for AI agents

![](https://www.google.com/s2/favicons?domain=seqcraft.onrender.com&sz=96)

Other · seqcraft.onrender.com

## SeqCraft

In-browser molecular biology workbench. Agents can inspect plasmids, select regions, edit sequences and manage annotations.

[Open seqcraft.onrender.com](https://seqcraft.onrender.com/)

## Ask an agent to

-   List the features annotated on my plasmid
-   Reverse complement bases 120 to 450 for review
-   Create a new circular construct from a DNA sequence

## 57 tools

-   `seqcraft_analyze_primer`read-onlyuntrusted content
    
    Compute melting temperature, GC content, molecular weight, and exact IUPAC-compatible binding loci on the template construct.
    
    documentId: string?, sequence: string?, primerId: string?
    
-   `seqcraft_analyze_restriction_sites`read-onlyuntrusted content
    
    Search for recognition and cut sites of standard restriction enzymes (Type II and Type IIS, e.g. EcoRI, BamHI, BsaI, BsmBI, NotI, HindIII) on the target molecule. Returns 1-based coordinates \[start1, end1\]…
    
    documentId: string?, enzymeNames: array
    
-   `seqcraft_clear_selection`untrusted content
    
    Clear the active range selection and unselect any highlighted features or primers in the SeqCraft workspace.
    
-   `seqcraft_compare_documents`read-onlyuntrusted content
    
    Perform pairwise biological sequence comparison and alignment between two documents in the workspace. Returns identity percentage, nucleotide differences (substitutions, insertions, deletions), and feature…
    
    sourceDocumentId: string, targetDocumentId: string
    
-   `seqcraft_copy_region_between_documents`untrusted content
    
    Extract a nucleotide region \[sourceStart1, sourceEnd1\] from a source construct and stage its insertion into a target construct at targetPosition1. Stages a revision-locked transaction on the target construct.
    
    sourceDocumentId: string, sourceStart1: integer, sourceEnd1: integer, targetDocumentId: string, targetPosition1: integer, orientation: string?
    
-   `seqcraft_create_document`untrusted content
    
    Create a new sequence document in the SeqCraft workspace from a nucleotide string. Validates sequence alphabet (DNA/RNA IUPAC).
    
    name: string, sequence: string, alphabet: string?, topology: string?
    
-   `seqcraft_create_document_from_region`untrusted content
    
    Extract a nucleotide sub-region \[start1, end1\] from a construct and create a new independent construct in the workspace.
    
    sourceDocumentId: string?, start1: integer, end1: integer, name: string, orientation: string?, topology: string?
    
-   `seqcraft_delete_document`untrusted content
    
    Remove a document from the SeqCraft workspace. To prevent accidental deletion during exploration, you must explicitly set confirmDelete: true.
    
    documentId: string, confirmDelete: boolean
    
-   `seqcraft_detect_known_features`read-onlyuntrusted content
    
    Scan the active or specified sequence against SeqCraft built-in curated biological feature library (promoters, origins, antibiotic resistance markers, reporters, tags). Returns identified matches with positions and…
    
    documentId: string?
    
-   `seqcraft_domesticate_sequence`read-onlyuntrusted content
    
    Scan a sequence for internal Type IIS or standard restriction sites and return revision-bound synonymous mutation candidates to eliminate internal cut sites without altering protein translation. Follow up with…
    
    documentId: string?, enzymeId: string
    
-   `seqcraft_duplicate_document`untrusted content
    
    Create an independent, isolated working copy of an existing document. Useful for safe experimentation, staging edits without altering the original construct, and testing modifications.
    
    documentId: string?, newName: string?
    
-   `seqcraft_edit_sequence`untrusted content
    
    Stage an insertion, deletion, or replacement on a DNA/RNA molecule using 1-based closed coordinates. Evaluates biological consequences (CDS frames, amino acid translations, restriction sites) and stages a…
    
    documentId: string?, operation: object?, range1: object?, sequence: string?, rationale: string?
    
-   `seqcraft_execute_actions`untrusted content
    
    Execute a batch of SeqCraft tool actions in sequential order. Rejects recursion. If any action stages a sequence mutation (status: awaiting\_approval) or errors in stop\_on\_error mode, execution halts immediately…
    
    actions: array, mode: string?
    
-   `seqcraft_export_document`read-onlyuntrusted content
    
    Export the active or specified construct to standard bioinformatic formats: GenBank flat file (including all features and annotations), FASTA, or SeqCraft JSON format. Returns generated text, filename, revision, and…
    
    documentId: string?, format: string?
    
-   `seqcraft_export_sequence`read-onlyuntrusted content
    
    Export the active or specified construct to standard bioinformatic formats: GenBank flat file (including all features and annotations), FASTA, or SeqCraft JSON format. Returns generated text, filename, revision, and…
    
    documentId: string?, format: string?
    
-   `seqcraft_find_crispr_targets`read-onlyuntrusted content
    
    Scan sequence for CRISPR-Cas guide RNA target sites and protospacers across multiple Cas effectors (SpCas9, SaCas9, Cas12a/Cpf1, Cas12e/CasX). Computes on-target quality scores, GC balance, Pol III termination…
    
    documentId: string?, nuclease: string?, minQualityScore: integer?, maxResults: integer?
    
-   `seqcraft_find_orfs`read-onlyuntrusted content
    
    Search for open reading frames across all six reading frames using NCBI genetic code table 1 and a configurable minimum codon count.
    
    documentId: string?, minCodons: integer?
    
-   `seqcraft_focus_region`untrusted content
    
    Navigate, scroll, and center the editor view around a specific nucleotide region using 1-based closed coordinates \[start1, end1\]. Optionally selects the region or switches representation.
    
    documentId: string?, start1: integer, end1: integer, preferredView: string?
    
-   `seqcraft_generate_opentrons_protocol`read-onlyuntrusted content
    
    Compile a production-ready Python protocol for automated liquid handling on Opentrons OT-2 or Flex robots. Supports PCR master mix distribution and restriction digestion setups.
    
    mode: string, robotModel: string?, numReactions: integer?, reactionVolumeUl: number?, documentId: string?, forwardPrimer: string?, reversePrimer: string?, annealingTempC: number?, … (list cut; the site may define more)
    
-   `seqcraft_get_active_document`read-onlyuntrusted content
    
    Retrieve summary details, topological properties, annotations count, primers count, and revision metadata for the active or specified document.
    
    documentId: string?
    
-   `seqcraft_get_capabilities`read-only
    
    Discover SeqCraft scientific workflows, coordinate conventions (1-based closed \[start1, end1\]), privacy boundaries, approval rules, and suggested agent task sequences. Use this when planning a multi-step interaction…
    
-   `seqcraft_get_document_revision`read-onlyuntrusted content
    
    Query the current revision number and canonical SHA-256 sequence hash of a document. Essential for revision-locking proposals, avoiding race conditions, and verifying mutation commits.
    
    documentId: string?
    
-   `seqcraft_get_history`read-onlyuntrusted content
    
    Retrieve the change history log and undo/redo availability for the active or specified construct.
    
    documentId: string?
    
-   `seqcraft_get_pending_transaction`read-onlyuntrusted content
    
    Check the lifecycle state (awaiting\_approval, applied, rejected, or stale) and provenance of a staged sequence transaction. Call this after staging an edit with seqcraft\_edit\_sequence or candidate staging tools to…
    
    transactionId: string?
    
-   `seqcraft_get_selected_context`read-onlyuntrusted content
    
    Read the currently selected nucleotide sequence slice and overlapping biological features in 1-based closed coordinates. Use this to inspect what the human user or current selection is highlighting without retrieving…
    
    documentId: string?
    
-   `seqcraft_get_transaction_status`read-onlyuntrusted content
    
    Check the lifecycle state (awaiting\_approval, applied, rejected, or stale) and provenance of a staged sequence transaction. Call this after staging an edit with seqcraft\_edit\_sequence or candidate staging tools to…
    
    transactionId: string?
    
-   `seqcraft_get_workspace_context`read-onlyuntrusted content
    
    Read the current SeqCraft workspace state, including the active molecule, current selection, selected feature, pending transaction state, active view, and registered tool count. Preferred bootstrap tool for any task…
    
    includeDocumentList: boolean?
    
-   `seqcraft_import_from_database`untrusted content
    
    Fetch and import an authoritative biological sequence from a public repository (NCBI Nucleotide / GenBank, RefSeq, ENA, Addgene) by accession ID into the SeqCraft workspace. Use this tool whenever the user references…
    
    provider: string?, accession: string, format: string?, openAfterImport: boolean?
    
-   `seqcraft_import_sequence_text`untrusted content
    
    Import DNA/RNA sequence data into SeqCraft from FASTA, GenBank flat file, or raw sequence text. Creates and opens the construct(s) in the workspace.
    
    content: string, name: string?
    
-   `seqcraft_list_documents`read-onlyuntrusted content
    
    List all sequence constructs/documents currently loaded in the SeqCraft workspace with their IDs, names, topologies, lengths in base pairs, and revision numbers.
    
-   `seqcraft_list_features`read-onlyuntrusted content
    
    List all annotated biological features (CDS, promoters, genes, origins, resistance markers, tags) on the target construct with their coordinates \[start1, end1\], strand (+/-), type, and qualifiers.
    
    documentId: string?, type: string?
    
-   `seqcraft_list_primers`read-onlyuntrusted content
    
    List all custom oligonucleotides and primers configured for the target molecule, including their sequences, lengths, and binding positions.
    
    documentId: string?
    
-   `seqcraft_mutate_feature`untrusted content
    
    Create, update, delete, or batch-create biological annotations on the active or specified construct using 1-based closed coordinates \[start1, end1\]. Immediately updates document annotations and records revision…
    
    documentId: string?, action: string, feature: object?, features: array?, featureId: string?
    
-   `seqcraft_mutate_primer`untrusted content
    
    Create, auto-bind, update, or delete primers on the construct. Action "add\_from\_sequence" automatically validates the primer, finds binding loci on the template molecule, and attaches the primer to the document.
    
    documentId: string?, action: string, name: string?, sequence: string?, description: string?, primerId: string?, patch: object?
    
-   `seqcraft_plan_domestication`read-onlyuntrusted content
    
    Scan a sequence for internal Type IIS or standard restriction sites and return revision-bound synonymous mutation candidates to eliminate internal cut sites without altering protein translation. Follow up with…
    
    documentId: string?, enzymeId: string
    
-   `seqcraft_prepare_restriction_clone`untrusted content
    
    Simulate restriction cloning between an insert construct and a destination vector using compatible restriction enzyme sticky ends.
    
    insertDocumentId: string, insertEnzyme1: string, insertEnzyme2: string, vectorDocumentId: string, vectorEnzyme1: string, vectorEnzyme2: string
    
-   `seqcraft_propose_annotation`untrusted content
    
    Automatically detect and apply a known annotation match from the built-in database to the molecule.
    
    documentId: string?, matchIndex: integer
    
-   `seqcraft_redo`untrusted content
    
    Redo the previously undone sequence edit on the active or specified construct in SeqCraft history.
    
    documentId: string?
    
-   `seqcraft_restore_revision`untrusted content
    
    Stage restoration of a document to a historical snapshot in the undo stack. Stages a revision-locked transaction.
    
    documentId: string, historySnapshotIndex: integer
    
-   `seqcraft_reverse_complement_region`untrusted content
    
    Stage an in-place reverse complement of a sequence region \[start1, end1\] on the target molecule. Creates a revision-locked transaction for human review.
    
    documentId: string?, start1: integer, end1: integer
    
-   `seqcraft_rotate_origin`untrusted content
    
    Stage setting a new circular origin (position 1) on a circular plasmid. Re-indexes nucleotide coordinates and feature locations. Requires a circular topology and human review.
    
    documentId: string?, newOrigin1: integer, rationale: string?
    
-   `seqcraft_screen_biosecurity`read-onlyuntrusted content
    
    Run automated biosecurity reference pre-screening against diagnostic signature motifs of regulated Select Agents and Controlled Biological Toxins (Filoviruses, Poxviruses, Henipaviruses, Anthrax, Tularemia, Plague…
    
    documentId: string?
    
-   `seqcraft_search_sequence_database`read-onlyuntrusted content
    
    Search public biological sequence databases (NCBI Nucleotide / GenBank, RefSeq, ENA / EMBL-EBI, Addgene) for accession IDs, plasmid constructs, genes, or genomes matching a query. Returns compact candidate records…
    
    provider: string?, query: string, limit: integer?
    
-   `seqcraft_select_feature`untrusted content
    
    Select an existing biological feature/annotation on the active or specified document by its unique feature ID. Highlights the feature in the viewer and opens its properties in the inspector.
    
    featureId: string, documentId: string?
    
-   `seqcraft_select_range`untrusted content
    
    Select a continuous range of nucleotides on the active or specified molecule using 1-based closed coordinates \[start1, end1\]. Updates the visible editor selection for human and agent context sharing.
    
    documentId: string?, start1: integer, end1: integer
    
-   `seqcraft_select_sequence_range`untrusted content
    
    Select a continuous range of nucleotides on the active or specified molecule using 1-based closed coordinates \[start1, end1\]. Updates the visible editor selection for human and agent context sharing.
    
    documentId: string?, start1: integer, end1: integer
    
-   `seqcraft_set_active_document`untrusted content
    
    Switch the active document tab in the SeqCraft workspace. Use this when you want to view, inspect, or edit a different open construct.
    
    documentId: string
    
-   `seqcraft_set_active_view`untrusted content
    
    Switch the primary workspace visualization view tab. Available views: map (plasmid/linear map), sequence (base-level nucleotide editor), features (annotation table), primers (primer design panel), enzymes (restriction…
    
    view: string
    
-   `seqcraft_show_feature`untrusted content
    
    Highlight and focus a specific feature on the canvas / editor view and reveal its properties in the inspector panel.
    
    documentId: string?, featureId: string
    
-   `seqcraft_show_restriction_site`untrusted content
    
    Highlight a restriction enzyme cut site on the map and editor view.
    
    documentId: string?, siteId: string?, enzymeName: string?, occurrence: integer?, view: string?
    
-   `seqcraft_simulate_digest`read-onlyuntrusted content
    
    Simulate single or multi-enzyme restriction digestion on a circular plasmid or linear DNA. Returns predicted fragment sizes, fragment sequences, and terminal overhang types.
    
    documentId: string?, enzymeNames: array
    
-   `seqcraft_simulate_golden_gate`read-onlyuntrusted content
    
    Simulate Golden Gate multi-fragment assembly using Type IIS restriction enzymes (e.g. BsaI, BsmBI, AarI). Validates compatible overhang pairs, checks junction fidelity, and returns the assembled construct.
    
    documentIds: array, enzymeName: string?
    
-   `seqcraft_simulate_pcr`read-onlyuntrusted content
    
    Simulate exact-match in silico PCR on a linear or circular template. Returns predicted amplicon coordinates, lengths, GC content, and primer-pair melting temperatures.
    
    documentId: string?, forwardPrimer: string?, reversePrimer: string?
    
-   `seqcraft_stage_domestication_candidate`untrusted content
    
    Stage an exact synonymous mutation candidate returned by seqcraft\_domesticate\_sequence. Checks revision locking to ensure the molecule was not modified since analysis, then creates a revision-locked transaction for…
    
    candidateId: string, documentId: string?
    
-   `seqcraft_stage_sequence_transaction`untrusted content
    
    Stage an exact synonymous mutation candidate returned by seqcraft\_domesticate\_sequence. Checks revision locking to ensure the molecule was not modified since analysis, then creates a revision-locked transaction for…
    
    candidateId: string, documentId: string?
    
-   `seqcraft_undo`untrusted content
    
    Undo the most recent sequence edit on the active or specified construct in SeqCraft history.
    
    documentId: string?
    
-   `seqcraft_update_document_metadata`untrusted content
    
    Update metadata for a document, such as renaming it or changing its topology (linear <-> circular).
    
    documentId: string?, name: string?, topology: string?
    

Tools

57

Registered with

JavaScript

Scan finished

Oct 19, 2026

Tool names and descriptions are what seqcraft.onrender.com/ registered when we loaded it in Chrome 154 on Browser Use Cloud. The summary and the “ask an agent” lines are AI-written from them. To call the tools yourself, see [Chrome’s WebMCP docs](https://developer.chrome.com/docs/ai/webmcp). [How we found it](https://browser-use.com/webmcp#method).

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