DeepDNA local

Name: DeepDNA local
Author: alfonsoguv

by alfonsoguvversion 0.1.2i★ –iRuns on your computer

Registry nameai.deepdna/local

Install

Overview

Description from the maker (original English)

Reads a raw DNA file on your computer and reports the variants DeepDNA curates, with sources.

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi1 of 1 passedChecked from public information; code not scanned yet
UsageiNot measured yet★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs on your computer
Transport: stdio
Category: Other

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 1 of 1 passed
Runs on your computer with your user’s permissions (files, network, apps).
The registry lists no key to fill in.

You need

PyPIPython’s uv installed (for the uvx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Open Claude Desktop → Settings → Developer → Edit Config, and paste this into claude_desktop_config.json

{
  "mcpServers": {
    "local": {
      "command": "uvx",
      "args": [
        "deepdna-mcp"
      ]
    }
  }
}

Run this in your terminal

claude mcp add local -- uvx deepdna-mcp

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "local": {
      "command": "uvx",
      "args": [
        "deepdna-mcp"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "local": {
      "type": "stdio",
      "command": "uvx",
      "args": [
        "deepdna-mcp"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

This one runs on your computer, and ChatGPT can only connect to servers on the internet. Pick another app.

Your choice stays on this device in a cookie; no account needed.

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Runs on your computer; the tool list appears in your AI app after you install it.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 6, 2026

✓ Pass
Maker matches the repo
The registry name was verified against the domain deepdna.ai (the registry checks domain ownership)
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
– Not applicable
Endpoint responds
This one runs on your computer; there is no internet endpoint
– Not applicable
Sign-in with OAuth
Runs on your computer and uses local settings instead
… Not checked yet
No hidden instructions in tool descriptions
Runs on your computer; we can only read tool lists from internet endpoints

Compared with others in Otheri

More stars than 0% of the other 32435 servers in this category
Published to the registry more recently than 80% of the other 32435 servers in this category
Basic checks equal to or better than 100% of the other 32435 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is DeepDNA local safe?

It passed 1 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

It runs on your computer. Your AI app starts it when needed, and data does not pass through the maker’s servers (unless it calls an online service itself).

Is it still maintained?

The GitHub repo last changed –, and the latest version (0.1.2) reached the registry 8 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. You also need Python (uv) on your computer.

What can I use instead?

In the same category: Spec Driven Development, Remote Desktop Commander, Apify MCP Server

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README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

DeepDNA MCP server

A remote Model Context Protocol server that gives AI agents cited pharmacogenomic and gene-variant lookups, so answers can quote CPIC and DPWG guidance and its sources. This repository also holds a local package that reads a raw DNA file on the user's own computer; nothing from the file is sent to DeepDNA, but what the package reports becomes part of the conversation with the AI model.

https://deepdna.ai/mcp

Streamable HTTP, stateless, no API key, no account. Listed in the official MCP registry as ai.deepdna/knowledge.

Educational information only, not medical advice. The server reports what curated sources and guidelines say about a gene, a variant or a drug–gene pair. It does not diagnose, prescribe or recommend a dose.

Tools

Tool	What it returns
`list_genes`	The genes in the knowledge base, with a one-line summary and category for each
`lookup_gene`	Everything curated about one gene: function, key variants with rsIDs, phenotypes, drug interactions, what a consumer genotyping array can and cannot tell you, and sources
`lookup_variant`	One variant by dbSNP rsID: gene, star-allele or common name, alleles on the plus strand of GRCh37, effect, frequency note and sources. Takes the rsID only, never a genotype
`lookup_drug_gene`	Guidance for a gene, optionally for one drug: guideline (CPIC or DPWG where one exists), summary, phenotype groups and sources
`check_medications`	Splits a list of generic drug names into drugs with a curated record (gene, and a `basis` field: CPIC or DPWG guideline, drug label, or primary literature) and drugs not covered. Needs no genotype

All five tools are read-only.

Two prompts, medication_review and explain_variant, package the common questions for clients that show MCP prompts.

Coverage today is 12 genes: CYP2C19, CYP2C9, CYP2D6, SLCO1B1, VKORC1, UGT1A1, G6PD, MTHFR, COMT, HFE, APOE and BRCA1, with 51 curated drug–gene pairs across 11 of them: 40 cite a CPIC or DPWG guideline, the rest a drug label or the primary literature; the basis field in check_medications says which (guideline is null, or "drug label", when no guideline exists). It is a small, reviewed set, not a mirror of PharmGKB/ClinPGx. Every record lists its sources. The level field (the guideline's evidence grade) is null for every pair today.

Connect

Claude Code

claude mcp add --transport http deepdna https://deepdna.ai/mcp

Cursor (~/.cursor/mcp.json) and other clients that use an mcpServers file:

"mcpServers": { "deepdna": { "type": "http", "url": "https://deepdna.ai/mcp" } } }

VS Code (.vscode/mcp.json):

"servers": { "deepdna": { "type": "http", "url": "https://deepdna.ai/mcp" } } }

Claude Desktop and claude.ai: add https://deepdna.ai/mcp as a custom connector.

Gemini CLI (installs the remote, read-only server https://deepdna.ai/mcp as an extension, not the local package; gemini-extension.json is in this repo):

gemini extensions install https://github.com/alfonsoguv/deepdna-mcp

Try it without a client

curl -s https://deepdna.ai/mcp \

-H "Content-Type: application/json" \ -H "Accept: application/json, text/event-stream" \ -d '{"jsonrpc":"2.0","id":1,"method":"tools/call","params":{"name":"lookup_drug_gene","arguments":{"gene":"CYP2C19","drug":"clopidogrel"}}}'

The answer carries the CPIC recommendation for clopidogrel by CYP2C19 metabolizer group, the sources it was written from, and the disclaimer. The same data is available as plain REST, documented in the API docs and the OpenAPI spec:

GET https://deepdna.ai/api/v1/pgx/CYP2C19/clopidogrel

GET https://deepdna.ai/api/v1/variants/rs4244285

Read a raw DNA file on your own computer

The remote server takes no genotype: its tools have no field for one. For a raw DNA file there is a local package in this repository. It reads the file on the user's computer and reports what it shows at each position DeepDNA curates, with the cited records. Nothing from the file is sent to deepdna.ai: the package downloads the same public records for every user, and lookup_drug_gene sends only the gene and drug names. What read_dna_file returns (the letters and counts at the curated positions) becomes part of the conversation with the AI model your client uses, under that provider's terms.

Claude Code (needs uv; the package is on PyPI):

claude mcp add deepdna-local -- uvx deepdna-mcp@0.1.2

The plugin/ folder packages the same command as a Claude plugin, for Claude Code and for Cowork sessions on the user's computer.

Clients that use an mcpServers file (if the client cannot find uvx, put its full path, from which uvx, in command):

"mcpServers": { "deepdna-local": { "command": "uvx", "args": ["deepdna-mcp@0.1.2"] } } }

Tool	What it returns
`read_dna_file`	What a 23andMe, AncestryDNA or MyHeritage/FamilyTreeDNA export (.txt, .csv or .zip) shows at each curated position
`lookup_drug_gene`	Guidance for a gene, optionally for one drug, from the public API. Sends only the gene and drug names

Each position gets one of four states: read, no_call, not_in_file, or unexpected_letters (letters that fit neither the record nor its complement). A missing or unreadable position is unknown, never normal.
For positions the record marks as countable (no phasing or other variants are needed to read them), it gives how many copies of the variant allele the file shows, with the record's text and sources.
genes limits the answer to what the user asked about. APOE, BRCA1 and HFE are disease-risk genes: they are read only when named in genes, so the user chooses what to learn.
sex is needed only for some chromosome X positions (G6PD).
It checks the file's strand first: at least three positions that are not A/T or C/G must agree, and none disagree. A/T and C/G positions, whose two letters look the same on either strand, are counted only on a confirmed strand.

A count at one position is not a metabolizer status, a diplotype, a diagnosis or a dose. The tools tell the model never to suggest starting, stopping or changing a medication: that stays with the prescriber. VCF files are not supported.

Try it with: *"My 23andMe file is at /Users/me/Downloads/genome.txt. What does it show at the CYP2C19 positions DeepDNA curates, and what do the sources say about clopidogrel?"* (on Windows, a path such as C:\Users\me\Downloads\genome.txt).

What it is not

The remote server does not read DNA files. DeepDNA does not parse DNA files on its servers; to read one, use the local package above. A remote lookup carries a gene symbol, an rsID or a drug name. Its tools have no genotype field, and an undeclared argument is refused and not used. The alleles it reports are on the plus strand of GRCh37, as 23andMe raw data reports them.
Neither server calls phenotypes or doses. Turning a genotype into a metabolizer status needs phasing and the other variants in the gene, which a single lookup or a chip file does not give. Tools such as PharmCAT do that from a VCF.
Remote usage is counted, people are not. Each request to the remote server is counted (method, tool, the lookup label described below, whether there was an answer, the client's name and version, its user-agent, a country code). IP addresses, request bodies and medication lists are not stored. A value typed into a declared field is recorded only as a short lookup label: an rsID in the form rs123, a gene from a fixed list of known pharmacogenes, or a drug DeepDNA covers; anything else, whatever it is, is recorded as "(other)". Please don't type a personal genetic result into these fields. See the privacy policy. The local package's downloads are ordinary requests to the public API, with the user-agent deepdna-mcp-local/ .
A consumer chip is not a clinical test. Arrays are reliable for common variants and much less so for rare ones; anything that could affect a health decision needs a validated test and a clinician.

Links

Docs: https://deepdna.ai/docs/#mcp
Walkthrough with real outputs: https://deepdna.ai/blog/pharmacogenomics-mcp-server/
Reading a 23andMe file with Claude using the local package, step by step: https://deepdna.ai/blog/read-23andme-file-with-claude/
Worked example in Python, where your own code goes from a raw DNA file to CPIC phenotypes (neither server does this step): https://deepdna.ai/blog/pharmacogenomics-raw-dna-python/
Terms: https://deepdna.ai/terms/ · Privacy: https://deepdna.ai/privacy/

This repository holds the documentation and the local package; the remote server is hosted by DeepDNA. Questions and bug reports go in the issues; please don't post a raw DNA file, genotypes or medications there.

Written with AI assistance.

DeepDNA local

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Otheri

Common questions

Alternatives

Spec Driven Development

Remote Desktop Commander

Apify MCP Server

README from the maker

DeepDNA MCP server

Tools

Connect

Try it without a client

Read a raw DNA file on your own computer

What it is not

Links