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Motif capabilities

What Motif can do today, grouped by area. Each line points at the code that backs it, so the list stays honest.

Sequence I/O and formats

  • Import raw DNA, RNA, and protein, FASTA, GenBank, Motif JSON, and AB1/ABI.
  • Export raw sequence, FASTA and multi-FASTA, basic GenBank/GFF3, CSV, JSON, Markdown/HTML/print reports, and a workspace ZIP.
  • Source: src/bio/fasta-parser.ts, src/bio/genbank-parser.ts, src/artifacts/motif-artifact.tsx.

Records and inventory

  • Create, group, tag, edit, and delete annotated records with features and notes.
  • Substitutions, insertions, deletions, reverse complement, and undo/redo, with a session workflow history.
  • Source: src/bio/mutate.ts, src/artifacts/claude-science-workspace-collections.ts.

Maps

  • Topology-aware circular and linear SVG maps with features, coordinates, restriction sites and clusters, selections, labels, and pan/zoom.
  • Source: src/components/plasmid-map/, src/plasmid-map/layout.ts.

Restriction, digest, and gel

  • Scan bundled and custom enzymes (including Type IIS), filter by source, predict linear and circular digests, and materialize fragment records.
  • Render a qualitative agarose gel with ladders.
  • Source: src/bio/restriction-sites.ts, src/artifacts/claude-science-digest-workflow.ts, src/artifacts/claude-science-gel-preview.ts.

Cloning and assembly

  • Gibson overlap planning, Golden Gate (kits, internal-site checks, fusion compatibility), GoldenBraid TU and alpha/omega workflows, and explicit sticky/blunt ligation, all with saveable plans and products.
  • Source: src/artifacts/claude-science-cloning-design.ts, src/bio/golden-gate.ts, src/bio/golden-braid.ts, src/artifacts/claude-science-assembly-workflows.ts.

Primer design and PCR

  • Rank primer pairs by Tm, GC, length, clamp, hairpin, and self/cross-dimer evidence; edit 5' tails; export FASTA; simulate PCR; hand off to cloning.
  • Source: src/artifacts/ClaudeSciencePrimerWorkspace.tsx, src/bio/primer-design.ts, src/bio/primer-thermodynamics.ts, src/bio/pcr.ts.

Alignment and MSA

  • Bounded in-browser star alignment, aligned FASTA/CLUSTAL import, consensus/conservation, identity, and mismatch navigation.
  • Nucleotide-to-protein alignment overlays currently use the Standard genetic code; record and feature genetic-code settings apply to the sequence workbench.
  • A no-shell helper runs MAFFT, MUSCLE, or Clustal Omega outside the browser and records engine, version, argv, and hashes.
  • Source: src/artifacts/claude-science-msa.ts, src/artifacts/ClaudeScienceMsaViewer.tsx, plugin scripts/run-msa.mjs.

Sanger and AB1

  • Parse and display the instrument base calls, Phred quality, peak positions, and four dye channels stored in AB1/ABI files; link traces to alignments; auto-orient reads; and review chromatograms and mismatches.
  • Source: src/bio/abi-import.ts, src/artifacts/ClaudeScienceSangerTraceViewer.tsx.

Analysis

  • ORF detection, GC and composition, Tm, molecular weight, and range or coding- feature translation with selectable supported NCBI genetic codes. A CDS/ORF /transl_table overrides its record default; unsupported explicit codes are preserved but block translation rather than silently falling back. Derived proteins and pinned amino-acid tracks retain the effective code. Source edits mark linked pinned tracks for review and block protein materialization until their range translation is explicitly confirmed.
  • Literal motif search and PAM-based CRISPR guide candidates.
  • Single-parent nucleotide products retain their record code. Multi-parent assembly products leave the code unset for explicit review instead of inferring expression context from their source fragments.
  • Source: src/bio/orf-detection.ts, src/bio/translate.ts, src/artifacts/motif-artifact.tsx.

Provenance, results, and checkpoints

  • Typed results for primer design, PCR, and assembly plans, plus storage and display of BLAST hits, structure models, reports, and tables, each with provenance, inputs, dependencies, and inert assets. Codex and other analysis tools can produce BLAST and structure-model results for Motif to organize and display.
  • Database JSON restores directly. A workspace ZIP holds the same inventory.json plus interchange exports; restore it by extracting inventory.json and loading it from Settings.
  • Browser downloads are reported as requests, not verified saves. Confirm the Database JSON or ZIP exists and can be reopened before treating it as a durable checkpoint.
  • Source: src/artifacts/claude-science-analysis-results.ts, src/artifacts/claude-science-session.ts.

Host connectors

  • A bounded full-workbench MCP App (motif_open_workbench) plus a fallback that returns a self-contained HTML artifact (motif_create_workbench_artifact).
  • Accepts Motif payloads, FASTA, GenBank, or raw sequence. The connector opens the workbench or returns a portable HTML resource; Codex can use its other tools for file operations and analysis programs.
  • The Codex plugin and Claude Science adapter package the same typed connector with host-specific installation and task guidance.
  • Source: mcp/motif/server.ts, mcp/motif/payload.ts, src/mcp-app/.

Runtime model

The Motif HTML workbench runs locally in the browser. The bundled alignment runner can invoke MAFFT, MUSCLE, or Clustal Omega with recorded engine identity, arguments, and hashes. Exports are portable files owned by the user.