SeqCraft

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_primerread-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_sitesread-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_selectionuntrusted content

  Clear the active range selection and unselect any highlighted features or primers in the SeqCraft workspace.

• seqcraft_compare_documentsread-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_documentsuntrusted 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_documentuntrusted 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_regionuntrusted 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_documentuntrusted 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_featuresread-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_sequenceread-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_documentuntrusted 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_sequenceuntrusted 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_actionsuntrusted 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_documentread-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_sequenceread-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_targetsread-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_orfsread-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_regionuntrusted 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_protocolread-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_documentread-onlyuntrusted content

  Retrieve summary details, topological properties, annotations count, primers count, and revision metadata for the active or specified document.

  documentId: string?

• seqcraft_get_capabilitiesread-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_revisionread-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_historyread-onlyuntrusted content

  Retrieve the change history log and undo/redo availability for the active or specified construct.

  documentId: string?

• seqcraft_get_pending_transactionread-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_contextread-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_statusread-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_contextread-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_databaseuntrusted 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_textuntrusted 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_documentsread-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_featuresread-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_primersread-onlyuntrusted content

  List all custom oligonucleotides and primers configured for the target molecule, including their sequences, lengths, and binding positions.

  documentId: string?

• seqcraft_mutate_featureuntrusted 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_primeruntrusted 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_domesticationread-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_cloneuntrusted 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_annotationuntrusted content

  Automatically detect and apply a known annotation match from the built-in database to the molecule.

  documentId: string?, matchIndex: integer

• seqcraft_redountrusted content

  Redo the previously undone sequence edit on the active or specified construct in SeqCraft history.

  documentId: string?

• seqcraft_restore_revisionuntrusted 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_regionuntrusted 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_originuntrusted 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_biosecurityread-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_databaseread-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_featureuntrusted 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_rangeuntrusted 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_rangeuntrusted 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_documentuntrusted 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_viewuntrusted 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_featureuntrusted 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_siteuntrusted 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_digestread-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_gateread-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_pcrread-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_candidateuntrusted 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_transactionuntrusted 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_undountrusted content

  Undo the most recent sequence edit on the active or specified construct in SeqCraft history.

  documentId: string?

• seqcraft_update_document_metadatauntrusted content

  Update metadata for a document, such as renaming it or changing its topology (linear <-> circular).

  documentId: string?, name: string?, topology: string?