Molecular biology

Motif is a molecular-biology workbench inside Claude Science.

Open a sequence, annotate it, align it against others, translate it, or compute its reverse complement — without leaving Claude Science. If you need an enzyme, codon table, or analysis Motif doesn't have, ask Claude to add it.

Set up in Claude Science View on GitHub
Runs in your browser Open source · MIT Claude can add tools
The Motif workbench: a three-pane view with a sequence inventory, a nucleotide sequence pane, and a circular pUC19 plasmid map with labeled features, on a warm cream background.
Watch

Ask Claude Science for an analysis, and Motif opens the result.

Claude annotates the common KRAS hotspot mutations in Motif, aligns them, and places CRISPR guide sequences on the map. It then reads a paper describing the vanillin pathway's final enzyme and builds that enzyme as a gene cassette. Plays with sound.

A Claude Science session · 2:21, with voiceover
Get started

Run Motif in Claude Science.

Motif runs from a local checkout. You need Node 22.12+ and permission for Claude Science to read the Motif folder.

Fastest path

Hand it to Claude Code.

Open Claude Code in a new folder and paste this:

Set up Motif for Claude Science from https://github.com/jvogan/motif

Claude Code reads the setup guide, clones the repo, installs dependencies, and registers the connector. You then grant the folder and reconnect in Claude Science — steps 3 to 5 below.

Or run each step yourself.

  1. Get the code

    Clone the repository and install dependencies.

    # needs Node 22.12+
git clone https://github.com/jvogan/motif
cd motif && npm ci

  2. Build and register the connector

    One command builds Motif and adds the local connector.

    npm run claude-science:setup

  3. Grant the folder in Claude Science

    Open Permissions and grant the exact Motif folder.

    A dialog asking to access the Motif folder on your computer, with read-only and read and write options and Allow and Deny buttons.
    Grant the folder as read-only or read and write.

  4. Relaunch and reconnect

    Fully quit and reopen Claude Science, then reconnect motif-local.

  5. Confirm, then try it

    motif-local appears under Connectors, in the Custom group. Ask Claude Science to open a sequence — for example, Open pUC19 in Motif.

    Claude Science asking to run the Motif open workbench tool, with Allow for this project and Deny buttons.
    Approve the tool call, or choose how long the approval lasts.
The workbench

Motif opens pUC19 with its sequence and circular map in sync.

Add a feature, search for a sequence pattern, mark the restriction sites, design CRISPR guides, and export it. Plays with sound.

The Motif workbench on pUC19 · 1:37, with voiceover
A worked example

One prompt loads a pathway's 44 proteins.

Ask Claude Science to find a pathway's genes and open them in Motif. Inspect the proteins, then align the ones you choose.

  1. Ask for the pathway

    Give Claude Science a UniProt entry. It identifies BCO1, finds its Reactome pathway (retinoid metabolism and transport), and fetches the participating genes.

    Claude Science reading a UniProt link, identifying BCO1 and its retinoid-metabolism Reactome pathway, and fetching the pathway's genes.
    UniProt Q9HAY6 → Reactome R-HSA-975634 · retinoid metabolism

  2. Load the pathway's proteins

    Claude loads their 44 protein sequences. GPC1's 558-residue sequence and protein map open in the workbench.

    The Motif workbench with 44 pathway proteins in the inventory and GPC1's amino-acid sequence and protein map open.
    44 proteins · GPC1 (P35052) · 558 aa

  3. Align the proteins

    Select the proteins you want and run a multiple sequence alignment in the browser, or export them to MAFFT, MUSCLE, or Clustal Omega.

    Motif's Multiple Sequence Alignment dialog with pathway proteins selected and options to align in the browser or export to external aligners.
    Align in browser · or MAFFT / MUSCLE / Clustal Omega

  4. Read the alignment

    Motif saves the BCO1–GPC1 alignment alongside its source sequences: 592 columns with conserved positions, a consensus row, and per-column differences. You can export it as aligned FASTA.

    A rendered multiple sequence alignment of BCO1 against GPC1: 592 columns with conserved positions, a consensus row, and per-column differences.
    BCO1 vs GPC1 · 592 columns · 20% conserved · export aligned FASTA
Overview

Map a plasmid, annotate its features, and translate its genes.

Ask Claude for a sequence and it opens in Motif as a circular or linear map. Add and edit features on the sequence, see every restriction site marked, and translate a gene to protein in frame. Plays with sound.

pUC19 in the Motif workbench · 0:35
Cloning & maps

Plan a construct before you build it.

Screen a plasmid against 154 built-in restriction enzymes, plus any Claude adds. Find the unique cutters, preview the fragments, and plan a Gibson or Golden Gate assembly with internal Type IIS sites flagged.

The Motif workbench on an 11,429 bp record: named restriction sites (HpaII/MspI, TaqI, HaeIII, AluI, XhoI) marked on the sequence, a linear map covered in restriction ticks with the crtE feature, and a digest preview reading 13 cuts and 14 fragments across 292 sites and 34 enzymes.
crtE (DQ012943) · 292/292 sites, 34 enzymes · digest preview 13 cuts, 14 fragments
  • Restriction digest with fragment sizes and cut positions
  • Primer design with Tm / GC tuning and enzyme-tail presets
  • Gibson & Golden Gate planning with compatible-overhang checks
Capabilities

Motif runs its analyses in your browser.

Claude adds enzymes, codon tables, and new analyses on request.

Read & inspect

The map and the sequence stay in sync.

  • Circular plasmid maps
  • Feature annotations
  • Reading-frame overlays
  • Live GC & length stats

Cut & clone

Plan a construct and check it for conflicts.

  • Restriction digest
  • Primer design (Tm / GC)
  • Gibson & Golden Gate
  • PCR simulation

Analyze

The same sequence gives the same numbers every time.

  • Six-frame ORF detection
  • GC, Tm & composition
  • NCBI genetic-code selection
  • Motif search, both strands

Transform

Turn one sequence into another and keep its history.

  • Range & feature translation
  • Reverse complement
  • Derived protein sequences
  • Parent & provenance notes

Import & export

Read and write FASTA and GenBank, or save the workspace as one file.

  • FASTA
  • GenBank
  • Raw sequence
  • Self-contained workspace

How Claude connects

Two connector tools open your sequences as a workbench, or save them as one HTML file.

  • FASTA, GenBank & raw sequence
  • Workbench or a single HTML file
  • Inspect and export results
  • Claude adds enzymes, codon tables & analyses
Advanced

Script the standalone workbench.

The standalone workbench exposes a documented page-local API: scripts can read the sequence on screen, load new records, and run their own checks.

// inspect the page-local contract and active record
window.motifHelp()
window.motifGetActiveRecord()
In Claude Science

Motif runs as a local connector in Claude Science.

npm run claude-science:setup registers the server. Grant the folder, choose how approvals work, then ask Claude Science to open a sequence.

The Claude Science Connectors list, Custom group, showing motif-local added and enabled.
Connectors → Custom · motif-local, enabled

Setup adds one connector, motif-local, under Connectors in the Custom group.

The motif-local connector detail in Claude Science: a Skip approvals toggle and two read-only tools, motif_open_workbench and motif_create_workbench_artifact.
motif-local · approvals and its two tools

Open motif-local to see its two tools, motif_open_workbench and motif_create_workbench_artifact. Leave approvals on and Claude Science shows a card before each call. Turn on Skip approvals to run them without prompting.

One session

Claude reads a paper and aligns its genes in Motif.

Paste a paper into Claude Science and ask Claude to open the genes it describes in Motif. Then ask for the same genes from other species, and for an alignment comparing them.

  1. Ask in plain language

    Paste a paper and ask Claude Science to open its genes in Motif.

    A Claude Science prompt asking it to open the genes characterized in a PLOS ONE paper in Motif.
    PLOS ONE · 10.1371/journal.pone.0096626

  2. Claude identifies and fetches

    It reads the paper, identifies the two characterized genes, FPS and crtE, and fetches their annotated GenBank records from NCBI.

    Claude Science listing FPS (KJ140284.1) and crtE (DQ012943.1) with their enzymes and lengths, and reporting the workbench opened with 2 records and 14,314 residues.
    FPS KJ140284.1 · crtE DQ012943.1 · 14,314 residues

  3. Open in the Motif viewer

    Both genes open in the workbench. The Inventory panel lists them; Sequence and Map show whichever one you select, with restriction sites and gene, mRNA, and CDS features.

    The Motif workbench open in Claude Science's right pane: the crtE record (DQ012943), its sequence with restriction sites, and an 11,429 bp linear map.
    motif_FPS_crtE.html · Inventory · Sequence · Map

  4. Add homologs in the same conversation

    Claude retrieves two more crtE and two more FPS homologs from UniProt, then opens a new workbench with all six.

    The Motif workbench grown to six records after a follow-up request: the two paper genes as DNA plus four UniProt protein homologs (BTS1, crtE, ERG20, FPS).
    6 sequences · 2 from the paper + 4 from UniProt

  5. Align all six

    Ask for a multiple sequence alignment. Claude Science runs Clustal Omega, and the alignment opens in Motif.

    Motif's MSA viewer showing a six-protein Clustal Omega alignment: 6 rows, 440 columns, with per-row identity, consensus, and conserved-column shading.
    6 rows · 440 columns · Clustal Omega 1.2.4
If setup gets stuck

Common problems and their fixes.

Most setup problems come from Claude Science's sandbox blocking the Motif folder. The troubleshooting guide covers the rest.

“Operation not permitted,” or the tools won't load
Claude Science's sandbox is blocking the folder. Open Permissions in Claude Science and grant the exact Motif folder, then fully quit and reopen the app. Reconnect alone does not apply a new grant.
The tool ran, but no workbench appeared
A text summary or resource link means the tool ran but no workbench was mounted. Ask Claude to create a Motif workbench artifact — for example, “please open this in the Motif workbench” — and Claude generates an HTML artifact that opens in the right pane.
The sequence shows as plain text
This is Claude Science's generic fallback display. Open the generated workbench artifact to see the sequence rendered.
The connector shows up, but its tools are missing
Rebuild, then reconnect the existing motif-local entry rather than adding a new one. If a tool's inputs or schema changed, relaunch Claude Science and start a fresh kernel so the new definition loads.
Node installed through nvm or asdf gets denied
A Node binary inside a version manager is often outside the granted folder. Use a system or Homebrew Node 22.12+, or grant that Node's folder and rerun setup with its path. The troubleshooting guide shows the command.

Open Motif in Claude Science.

Load a plasmid, inspect the maps and digests Claude builds, and ask for the next analysis.

Set up in Claude Science Read the docs on GitHub