Ensembl MCP Server

Name: Ensembl MCP Server
Author: cyanheads

by cyanheadsversion 0.7.1i★ –iComputer or cloud

Registry nameio.github.cyanheads/ensembl-mcp-server

Install

Overview

Description from the maker (original English)

Look up genes, sequences, variants, homologs, and cross-database xrefs from Ensembl REST.

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 checksi3 of 3 passedChecked from public information; code not scanned yet
UsageiVery new↓ 164/wk · ★ –

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: Computer or cloud
Transport: stdio, Streamable HTTP
Category: Databases & datasets

Install

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

Before you install

Basic checks: 3 of 3 passed
Runs on the maker’s server: what you ask it goes through their server.
Can do 7 things (tools) ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence, ensembl_query_region …
You fill in yourself: ENSEMBL_BASE_URL, MCP_LOG_LEVEL

You need

Runs in the cloudNothing to install; it connects over the internet
npmNode.js installed (for the npx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

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

Works in Claude on the web, desktop and mobile:

Open Settings → Connectors
Press Add custom connector
Paste the address below and press Add
If it asks you to sign in, sign in with the maker

https://ensembl.caseyjhand.com/mcp

Or run it on your computer

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

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "your-value",
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

Run this in your terminal

claude mcp add --transport http ensembl https://ensembl.caseyjhand.com/mcp

Or run it on your computer

claude mcp add ensembl --env ENSEMBL_BASE_URL=your-value --env MCP_LOG_LEVEL=your-value -- npx -y @cyanheads/ensembl-mcp-server

Fill in the empty values before running it.

Open in Cursor

Or copy the settings yourself

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

{
  "mcpServers": {
    "ensembl": {
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Or run it on your computer

Open in Cursor

Or copy the settings yourself

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

{
  "mcpServers": {
    "ensembl": {
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "your-value",
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

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": {
    "ensembl": {
      "type": "http",
      "url": "https://ensembl.caseyjhand.com/mcp"
    }
  }
}

Or run it on your computer

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "ensembl": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@cyanheads/ensembl-mcp-server"
      ],
      "env": {
        "ENSEMBL_BASE_URL": "your-value",
        "MCP_LOG_LEVEL": "your-value"
      }
    }
  }
}

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.

ChatGPT connects only to servers on the internet:

Open ChatGPT on the web → Settings → Connectors (Apps)
Press Create or Add (some plans need Developer mode under Advanced first)
Paste the address below, give it a name and save
If it asks you to sign in, sign in with the maker

https://ensembl.caseyjhand.com/mcp

Menu names can differ slightly by plan and over time.

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

Values you fill in

ENSEMBL_BASE_URL env
Ensembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.
MCP_LOG_LEVEL env
Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

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

What it can do

Tool names and descriptions exactly as the server reported them on Nov 7, 2026. The maker wrote them, not us; we show them as plain text.

ensembl_list_species
List species supported by Ensembl with display name, common name, assembly, taxon ID, and division. Required discovery step — species names like homo_sapiens are opaque to non-biologists and are the input format every other Ensembl tool expects. Use nameContains to find a species
ensembl_lookup_gene
Resolve a gene by symbol + species (or by stable ID) to its Ensembl ID, genomic location (chr:start-end:strand), biotype, description, and transcript list. Entry point for most workflows — the stable ID and coordinates returned here are inputs to other tools. Accepts both symbol
ensembl_get_sequence
Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns a window of the sequence — the first 10,000 characters by default — with its stable ID, molecule type, and full length. When more follows the window, truncated is true and ne
ensembl_query_region
Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, plus the genome assembly the coordinates are on. Useful for "what's in this locus?" and
ensembl_predict_variant
Predict the functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP). Accepts three input formats: HGVS notation (transcript-relative, e.g. ENST00000380152.8:c.2T>A, or genomic, e.g. 13:g.32316462T>A); region+allele (chr:start:end:strand/alle
ensembl_get_homology
Find orthologs and/or paralogs of a gene across species. Returns each homolog's stable ID, species, homology type (ortholog_one2one, ortholog_one2many, paralog_many2many, etc.), percId and percPos (percent identical and positive positions, over the target protein's length), and t
ensembl_get_xrefs
Retrieve cross-database references for a gene or feature — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others. Returns each xref with its database name, primary ID, display ID, and description, plus how Ensembl assigned it (infoType, infoText) and its evidence codes (l

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 8, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account cyanheads, which owns the repo
… 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
✓ Pass
Endpoint responds
Responded in 498 ms (HTTP 200)
– Not applicable
Sign-in with OAuth
No sign-in needed
✓ Pass
No hidden instructions in tool descriptions
Read 7 tool descriptions and found no hidden instructions to the AI

Compared with others in Databases & datasetsi

More stars than 0% of the other 1146 servers in this category
Published to the registry more recently than 77% of the other 1146 servers in this category
Basic checks equal to or better than 100% of the other 1146 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 Ensembl MCP Server safe?

It passed 3 of 3 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?

Either way works: install it on your computer or connect to the cloud version.

Is it still maintained?

The GitHub repo last changed –, and the latest version (0.7.1) reached the registry 10 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. It connects by URL, so apps that accept remote MCP servers work too, such as ChatGPT in developer mode.

What can I use instead?

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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.

@cyanheads/ensembl-mcp-server Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP. 7 Tools • 4 Resources • 1 Prompt

Public Hosted Server: https://ensembl.caseyjhand.com/mcp

Overview

Gene, sequence, and variant data for vertebrates and other model organisms from the Ensembl REST API. Look up genes, fetch sequences, predict variant consequences, find orthologs, and cross-reference external databases.

Tools

Tool	Description
`ensembl_list_species`	List species supported by Ensembl with display name, common name, assembly, taxon ID, and division
`ensembl_lookup_gene`	Resolve a gene by symbol (synonyms and former symbols included) + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript list
`ensembl_get_sequence`	Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region
`ensembl_query_region`	Find genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal region
`ensembl_predict_variant`	Predict functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP)
`ensembl_get_homology`	Find orthologs and/or paralogs of a gene across species with percent identity and taxonomy level
`ensembl_get_xrefs`	Retrieve cross-database references for a gene — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others

Resources

Resource	Description
`ensembl://gene/{id}`	Gene record by stable ID (`ENSG…`) — location, biotype, description, and transcript list
`ensembl://transcript/{id}`	Transcript record by stable ID (`ENST…`) — parent gene, location, biotype, canonical flag, and length
`ensembl://species`	Supported Ensembl species for the endpoint default division (vertebrates on the default endpoint)
`ensembl://species/{division}`	Supported species in one division (`EnsemblVertebrates`, `EnsemblPlants`, `EnsemblFungi`, `EnsemblMetazoa`, `EnsemblProtists`)

The species resources return the first 50 species by internal name; the ensembl_list_species tool pages through the rest and filters by name.

Prompts

Prompt	Description
`ensembl_gene_dossier`	Structured workflow for assembling a complete gene profile: symbol → ID + location → sequence → variants → orthologs → xrefs

Capability reference

Ensembl's stable-ID endpoints answer a versioned ID (ENSG00000139618.19) as not found, so every tool and resource that takes an Ensembl stable ID drops a trailing .N from an ENS… ID before the request and returns the current version. HGVS input to ensembl_predict_variant (ENST00000380152.8:c.2T>A) keeps its version, and IDs from other sources (AT3G52430.1) are forwarded unchanged.

`ensembl_list_species` tool

Optional division (EnsemblVertebrates, EnsemblPlants, EnsemblFungi, EnsemblMetazoa, EnsemblProtists; omitted, the endpoint default — vertebrates, ~356 species on GRCh38) and nameContains, a substring match against name, display name, and common name
Returns the internal name every other tool expects (homo_sapiens), plus display name, common name, taxon ID, assembly, and division
Sorted by internal name and paged by offset (default 0) and max_results (default 50, 0 uncapped); totalCount reports every match, and nextOffset is where the next page starts when more follow

`ensembl_lookup_gene` tool

Exactly one of symbol (+ species, default homo_sapiens), id, ids, or symbols (up to 1,000 submitted items; first 20 distinct trimmed queries processed); expand_transcripts (default false) adds the transcript list with biotype and canonical flag
canonicalTranscript identifies the canonical transcript without expansion; transcript-ID lookups also return parentGeneId. Expanded transcripts include maneSelect RefSeq accessions when available (BRCA2: ENST00000380152.8, NM_000059.4)
A symbol that is not a current gene name falls back to synonyms and former symbols (HER2 → ERBB2), reported as matchedAlias; a name shared by several genes (MDR1) returns ambiguous with candidates to retry by id
A single lookup returns gene (or ambiguous); a batch returns ordered succeeded items carrying the submitted query, failed items with query, reason (not_found, ambiguous with candidates, or unavailable), error, and recovery, and omitted queries past the processing cap. Omitted queries are never requested or reported as failed; resubmit them separately. Errors: not_found, invalid_species, no_input, conflicting_input

`ensembl_get_sequence` tool

A stable ID (ENSG…/ENST…/ENSP…) or a region (species:chr:start-end, or chr:start-end with species; at most 10,000,000 bases); type is genomic (default), cdna, cds, or protein — cdna and cds from a transcript ID only, protein from a transcript or protein ID; expand_5prime/expand_3prime add flanking bases
Regions take a :1/:-1 strand suffix (1:1000000-1000020:-1 returns the reverse complement); the mitochondrion is MT in vertebrates (mitochondrion_genome in Drosophila, MtDNA in C. elegans), and M/chrM are rejected as invalid_region where they would not resolve to it
Returns a window set by offset (default 0) and max_length (default 10000, 0 uncapped); length is the full sequence length, and truncated/nextOffset say where to resume
Errors: not_found, type_mismatch (also a protein ID asked for genomic/cdna/cds, or a non-coding transcript asked for protein/cds), invalid_species, missing_species, invalid_region (also an id with a colon that is not a valid region)

`ensembl_query_region` tool

region as species:chr:start-end, or chr:start-end with species (at most 5,000,000 bases; reversed coordinates are rejected; mitochondrion naming as in ensembl_get_sequence); feature defaults to ["gene"] and also accepts transcript, variation, regulatory, exon; optional case-sensitive biotype filter (protein_coding, lncRNA). An empty filtered result suggests removing the filter without inferring the locus is intergenic
max_results caps the list (default 100, 0 uncapped) while totalCount reports the true count; assemblyName names the coordinates' assembly, and exon rows carry parentId and rank. Errors: invalid_region, invalid_species, missing_species

`ensembl_predict_variant` tool

variant as HGVS (transcript-relative or genomic), region+allele (chr:start:end:strand/allele), or a dbSNP rsID
Returns the most severe consequence, per-transcript impact (HIGH/MODERATE/LOW/MODIFIER), and colocated known variants with clinical significance. Errors: invalid_notation, not_found, invalid_species
Requests HGVS, canonical and MANE annotations on every input route. Consequences retain variantAllele, optional canonical/maneSelect, HGVS and available SIFT/PolyPhen prediction-score pairs; records retain alleleString
Colocated clinicalSignificance is aggregate, not a classification of the submitted allele. clinicalSignificanceByAllele preserves explicit per-allele terms and clinicalSignificanceReferenceAllele identifies their reference allele; absent annotations remain omitted
max_transcript_consequences and max_pubmed_ids_per_variant (default 10 each, 0 uncapped; include_all_colocated_pubmed lifts the PubMed cap) bound the result, while transcriptConsequencesTotal and pubmedTotal report the full counts

`ensembl_get_homology` tool

Exactly one of symbol (+ species, default homo_sapiens) or id; type is orthologues (default), paralogues, or all; optional target_species filter
A target_species outside the comparison Ensembl runs for the source species (a fly gene to homo_sapiens) is answered from Ensembl's pan-taxonomic comparison when it holds both species, with a notice saying so
max_results caps the list (default 25, 0 uncapped) while totalCount reports the true count. Errors: not_found, invalid_species (unknown species or target_species), target_not_compared (a target outside the source species' comparison that the pan-taxonomic comparison cannot answer), no_input, conflicting_input
Each row retains optional targetProteinId for ensembl_get_sequence with type:"protein". Optional targetSymbol comes from a lookup of the returned rows' distinct gene IDs, in chunks of at most 1,000, with one five-second budget bounded by the call's remaining deadline and no retries. Missing names or failed lookups retain every primary homolog with a notice; cancellation still aborts

`ensembl_get_xrefs` tool

id (ENSG…/ENST…/ENSP…) required; optional dbname filter (e.g. HGNC, Uniprot_gn, Uniprot/SWISSPROT for the reviewed UniProt accession on the translation, EntrezGene, MIM_GENE, RefSeq_mRNA, Reactome_gene for gene pathways, Reactome for translation pathways, GO)
Default all_levels:false queries the requested object's level. Set all_levels:true to include a gene's transcript and translation references, independently of dbname; for example, gene-level RefSeq_mRNA may need this or a transcript ID. Empty lists remain successful with totalCount:0. Errors: not_found
Each reference carries how Ensembl assigned it (infoType: DIRECT, DEPENDENT, PROJECTION, …; infoText: its source, such as UniProt or the ortholog a projection came from) and its evidence codes (linkageTypes, GO evidence such as IDA or IEA) when su

Only the beginning is shown; read the rest in the repo

Ensembl MCP Server

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

Or run it on your computer

Or run it on your computer

Or run it on your computer

Or run it on your computer

Values you fill in

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 Databases & datasetsi

Common questions

Alternatives

Supabase

MongoDB MCP Server

Elasticsearch MCP Server

README from the maker

Overview

Tools

Resources

Prompts

Capability reference

ensembl_list_species tool

ensembl_lookup_gene tool

ensembl_get_sequence tool

ensembl_query_region tool

ensembl_predict_variant tool

ensembl_get_homology tool

ensembl_get_xrefs tool

`ensembl_list_species` tool

`ensembl_lookup_gene` tool

`ensembl_get_sequence` tool

`ensembl_query_region` tool

`ensembl_predict_variant` tool

`ensembl_get_homology` tool

`ensembl_get_xrefs` tool