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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 instrument base calls, Phred quality, peak positions, and four dye channels; link traces to alignments; auto-orient reads; view chromatograms and mismatches. It reads existing calls and does not re-basecall.
  • 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 externally produced BLAST hits, structure models, reports, and tables, each with provenance, inputs, dependencies, and inert assets. Motif does not compute BLAST searches or structure models inside the HTML.
  • 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.

Claude Science connector

  • 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. It does not write a database, run external executables, or expose a generic DOM/shell/filesystem bridge.
  • Source: mcp/motif/server.ts, mcp/motif/payload.ts, src/mcp-app/.

Boundaries

Motif is a design and inspection bench, not a validation service. The HTML runs locally and cannot launch native executables. Exports are ordinary user-owned files, not an encrypted or durable shared database. External alignment engines run only when explicitly invoked through the bundled runner.