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seqcraft.onrender.com

Read 1 time since 12 Oct 2026. Last read 12 Oct 2026.

57

tools offered to AI agents, on the record.

https://seqcraft.onrender.com/

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Tools

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  1. seqcraft_analyze_primerReads only

    Compute melting temperature, GC content, molecular weight, and exact IUPAC-compatible binding loci on the template construct.

    First seen 12 Oct 2026. Unchanged since.

  2. seqcraft_analyze_restriction_sitesReads only

    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], forwardCut1, reverseCut1, and overhang types.

    First seen 12 Oct 2026. Unchanged since.

  3. seqcraft_clear_selectionCan change things

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

    First seen 12 Oct 2026. Unchanged since.

  4. seqcraft_compare_documentsReads only

    Perform pairwise biological sequence comparison and alignment between two documents in the workspace. Returns identity percentage, nucleotide differences (substitutions, insertions, deletions), and feature discrepancies.

    First seen 12 Oct 2026. Unchanged since.

  5. seqcraft_copy_region_between_documentsCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  6. seqcraft_create_documentCan change things

    Create a new sequence document in the SeqCraft workspace from a nucleotide string. Validates sequence alphabet (DNA/RNA IUPAC).

    First seen 12 Oct 2026. Unchanged since.

  7. seqcraft_create_document_from_regionCan change things

    Extract a nucleotide sub-region [start1, end1] from a construct and create a new independent construct in the workspace.

    First seen 12 Oct 2026. Unchanged since.

  8. seqcraft_delete_documentCan change things

    Remove a document from the SeqCraft workspace. To prevent accidental deletion during exploration, you must explicitly set confirmDelete: true.

    First seen 12 Oct 2026. Unchanged since.

  9. seqcraft_detect_known_featuresReads only

    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 confidence.

    First seen 12 Oct 2026. Unchanged since.

  10. seqcraft_domesticate_sequenceReads only

    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 seqcraft_stage_domestication_candidate to stage a proposal for human review.

    First seen 12 Oct 2026. Unchanged since.

  11. seqcraft_duplicate_documentCan change things

    Create an independent, isolated working copy of an existing document. Useful for safe experimentation, staging edits without altering the original construct, and testing modifications.

    First seen 12 Oct 2026. Unchanged since.

  12. seqcraft_edit_sequenceCan change things

    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 revision-locked transaction for human review. Does NOT modify the molecule until the human clicks Apply. Follow up with seqcraft_get_transaction_status.

    First seen 12 Oct 2026. Unchanged since.

  13. seqcraft_execute_actionsCan change things

    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 without executing subsequent actions.

    First seen 12 Oct 2026. Unchanged since.

  14. seqcraft_export_documentReads only

    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 sequence hash.

    First seen 12 Oct 2026. Unchanged since.

  15. seqcraft_export_sequenceReads only

    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 sequence hash.

    First seen 12 Oct 2026. Unchanged since.

  16. seqcraft_find_crispr_targetsReads only

    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 penalties, and MMEJ frameshift predictions.

    First seen 12 Oct 2026. Unchanged since.

  17. seqcraft_find_orfsReads only

    Search for open reading frames across all six reading frames using NCBI genetic code table 1 and a configurable minimum codon count.

    First seen 12 Oct 2026. Unchanged since.

  18. seqcraft_focus_regionCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  19. seqcraft_generate_opentrons_protocolReads only

    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.

    First seen 12 Oct 2026. Unchanged since.

  20. seqcraft_get_active_documentReads only

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

    First seen 12 Oct 2026. Unchanged since.

  21. seqcraft_get_capabilitiesReads 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 or deciding which SeqCraft tools to call.

    First seen 12 Oct 2026. Unchanged since.

  22. seqcraft_get_document_revisionReads only

    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.

    First seen 12 Oct 2026. Unchanged since.

  23. seqcraft_get_historyReads only

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

    First seen 12 Oct 2026. Unchanged since.

  24. seqcraft_get_pending_transactionReads only

    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 check if the human approved the change.

    First seen 12 Oct 2026. Unchanged since.

  25. seqcraft_get_selected_contextReads only

    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 the entire molecule.

    First seen 12 Oct 2026. Unchanged since.

  26. seqcraft_get_transaction_statusReads only

    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 check if the human approved the change.

    First seen 12 Oct 2026. Unchanged since.

  27. seqcraft_get_workspace_contextReads only

    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 involving SeqCraft.

    First seen 12 Oct 2026. Unchanged since.

  28. seqcraft_import_from_databaseCan change things

    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 a known public accession (e.g. J01749.1, NC_001416.1, OQ870305.1) or asks SeqCraft to obtain a biological sequence from a public repository. Preserves sequence topology, GenBank annot

    First seen 12 Oct 2026. Unchanged since.

  29. seqcraft_import_sequence_textCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  30. seqcraft_list_documentsReads only

    List all sequence constructs/documents currently loaded in the SeqCraft workspace with their IDs, names, topologies, lengths in base pairs, and revision numbers.

    First seen 12 Oct 2026. Unchanged since.

  31. seqcraft_list_featuresReads only

    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.

    First seen 12 Oct 2026. Unchanged since.

  32. seqcraft_list_primersReads only

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

    First seen 12 Oct 2026. Unchanged since.

  33. seqcraft_mutate_featureCan change things

    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 provenance.

    First seen 12 Oct 2026. Unchanged since.

  34. seqcraft_mutate_primerCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  35. seqcraft_plan_domesticationReads only

    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 seqcraft_stage_domestication_candidate to stage a proposal for human review.

    First seen 12 Oct 2026. Unchanged since.

  36. seqcraft_prepare_restriction_cloneCan change things

    Simulate restriction cloning between an insert construct and a destination vector using compatible restriction enzyme sticky ends.

    First seen 12 Oct 2026. Unchanged since.

  37. seqcraft_propose_annotationCan change things

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

    First seen 12 Oct 2026. Unchanged since.

  38. seqcraft_redoCan change things

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

    First seen 12 Oct 2026. Unchanged since.

  39. seqcraft_restore_revisionCan change things

    Stage restoration of a document to a historical snapshot in the undo stack. Stages a revision-locked transaction.

    First seen 12 Oct 2026. Unchanged since.

  40. seqcraft_reverse_complement_regionCan change things

    Stage an in-place reverse complement of a sequence region [start1, end1] on the target molecule. Creates a revision-locked transaction for human review.

    First seen 12 Oct 2026. Unchanged since.

  41. seqcraft_rotate_originCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  42. seqcraft_screen_biosecurityReads only

    Run automated biosecurity reference pre-screening against diagnostic signature motifs of regulated Select Agents and Controlled Biological Toxins (Filoviruses, Poxviruses, Henipaviruses, Anthrax, Tularemia, Plague, BoNT, Ricin). Informational diagnostic screening only.

    First seen 12 Oct 2026. Unchanged since.

  43. seqcraft_search_sequence_databaseReads only

    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 with accession, title, organism, length in bp, and molecule type.

    First seen 12 Oct 2026. Unchanged since.

  44. seqcraft_select_featureCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  45. seqcraft_select_rangeCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  46. seqcraft_select_sequence_rangeCan change things

    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.

    First seen 12 Oct 2026. Unchanged since.

  47. seqcraft_set_active_documentCan change things

    Switch the active document tab in the SeqCraft workspace. Use this when you want to view, inspect, or edit a different open construct.

    First seen 12 Oct 2026. Unchanged since.

  48. seqcraft_set_active_viewCan change things

    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 digests), history (revision log), compare (sequence comparison/diff).

    First seen 12 Oct 2026. Unchanged since.

  49. seqcraft_show_featureCan change things

    Highlight and focus a specific feature on the canvas / editor view and reveal its properties in the inspector panel.

    First seen 12 Oct 2026. Unchanged since.

  50. seqcraft_show_restriction_siteCan change things

    Highlight a restriction enzyme cut site on the map and editor view.

    First seen 12 Oct 2026. Unchanged since.

  51. seqcraft_simulate_digestReads only

    Simulate single or multi-enzyme restriction digestion on a circular plasmid or linear DNA. Returns predicted fragment sizes, fragment sequences, and terminal overhang types.

    First seen 12 Oct 2026. Unchanged since.

  52. seqcraft_simulate_golden_gateReads only

    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.

    First seen 12 Oct 2026. Unchanged since.

  53. seqcraft_simulate_pcrReads only

    Simulate exact-match in silico PCR on a linear or circular template. Returns predicted amplicon coordinates, lengths, GC content, and primer-pair melting temperatures.

    First seen 12 Oct 2026. Unchanged since.

  54. seqcraft_stage_domestication_candidateCan change things

    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 human review.

    First seen 12 Oct 2026. Unchanged since.

  55. seqcraft_stage_sequence_transactionCan change things

    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 human review.

    First seen 12 Oct 2026. Unchanged since.

  56. seqcraft_undoCan change things

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

    First seen 12 Oct 2026. Unchanged since.

  57. seqcraft_update_document_metadataCan change things

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

    First seen 12 Oct 2026. Unchanged since.

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