Ensembl Mcp Server

cyanheads/ensembl-mcp-server

Connects Claude to the Ensembl REST API for genomic lookup and analysis. You get seven tools covering gene resolution by symbol or stable ID, sequence retrieval in multiple formats (genomic, cDNA, CDS, protein), variant consequence prediction via VEP, homology searches across species, and cross-database reference lookups to HGNC, UniProt, and OMIM. Also includes region queries for finding overlapping features and a species catalog tool since Ensembl expects names like homo_sapiens. Supports both stdio and streamable HTTP, with a public hosted instance at ensembl.caseyjhand.com. Reach for this when you need to translate gene symbols into stable IDs, pull sequences with flanking regions, predict variant effects in HGVS notation, or chain into pathway and protein databases via xrefs.

GitHub stars: 3
tools: 7
transport: STDIO, HTTP
env vars: 7
last updated: Oct 29, 2026

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Install

From registry metadata

$ npx add-mcp https://ensembl.caseyjhand.com/mcp --name ensembl

Run in your terminal. add-mcp asks which agents to add it to (Claude Code, Codex, Cursor and more). Add -g to install it for every project.

Review the command, arguments and environment values before installing. MCP servers run with your local permissions.

Other ways

Claude Code

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

Run in your terminal. Add --scope user to make it available in every project.

Tools

Verified live · 7 tools

Verified live against the running server on Nov 6, 2026.

ensembl_list_speciesList 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 spec...4 params

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 spec...

Parameters* required

divisionstring

Filter to a specific Ensembl division. EnsemblVertebrates includes human, mouse, zebrafish, and other vertebrates. EnsemblPlants covers crop and model plant genomes. EnsemblFungi, EnsemblMetazoa, E...one of EnsemblVertebrates · EnsemblPlants · EnsemblFungi · EnsemblMetazoa · EnsemblProtists

max_resultsinteger

Maximum number of species to return, counted from offset. Default 50. Set to 0 to return every matching species from offset to the end, uncapped. totalCount always reports the full number of matche...default: 50

nameContainsstring

Case-insensitive substring filter applied locally after fetching. Matches against species name, display name, and common name. Example: "sapiens" matches homo_sapiens; "mouse" matches mus_musculus.

offsetinteger

0-based position in the name-sorted matches where the returned page starts. Default 0. Pass nextOffset from a previous response to fetch the following page; an offset at or past totalCount returns...default: 0

ensembl_lookup_geneResolve 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 symb...6 params

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 symb...

Parameters* required

expand_transcriptsboolean

When true, include the full transcript list in the response. Each transcript has its ID, biotype, canonical flag, and coordinates. Default is false to keep responses compact.default: false

idstring

Ensembl stable gene ID (e.g. ENSG00000139618). A version suffix on an ENS… ID (ENSG00000139618.19) is dropped before the lookup, which returns the current version. Species is not required for ID lo...

idsarray

Batch submission: up to 1,000 Ensembl stable IDs (ENSG…, ENST…); resolves the first 20 distinct trimmed queries. batch.omitted names the remainder to resubmit. A version suffix on an ENS… ID is dro...

speciesstring

Species in Ensembl internal format: lowercase scientific name with underscores (e.g. homo_sapiens, mus_musculus, danio_rerio). Optional for symbol lookups — defaults to homo_sapiens; set it for oth...

symbolstring

Gene symbol to look up (e.g. BRCA2, TP53, EGFR). Species defaults to homo_sapiens; set species for other organisms. Case-insensitive in most species. A synonym or former symbol (HER2, TB1) resolves...

symbolsarray

Batch submission: up to 1,000 gene symbols; resolves the first 20 distinct trimmed queries. batch.omitted names the remainder to resubmit. Species defaults to homo_sapiens; set species for other or...

ensembl_get_sequenceFetch 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...7 params

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...

Parameters* required

expand_3primeinteger

Number of base pairs to extend downstream (3' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries; on a :-1 region it extends the lower coordinate.default: 0

expand_5primeinteger

Number of base pairs to extend upstream (5' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries; on a :-1 region it extends the higher coordinate.default: 0

id*string

Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode — an id containing a colon is a region. A version suffix on a stable ID (ENST00000380152.8) is dropped before the request...

max_lengthinteger

Maximum number of characters in the returned window. Default 10000. Set to 0 to return everything from offset to the end, uncapped.default: 10000

offsetinteger

0-based character offset where the returned window starts, counted in the resolved sequence (including any expand_5prime/expand_3prime flank). Default 0. Pass nextOffset from a truncated response t...default: 0

speciesstring

Species in Ensembl internal format (e.g. homo_sapiens). Required for a bare chr:start-end region. For the species:chr:start-end form the species in id takes precedence and this field is ignored. Un...

typestring

Sequence type to retrieve. genomic: full genomic DNA including introns (default). cdna: spliced transcript sequence (requires ENST… ID). cds: coding sequence only, no UTRs (requires ENST… ID with c...one of genomic · cdna · cds · proteindefault: genomic

ensembl_query_regionFind 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?"...5 params

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?"...

Parameters* required

biotypestring

Optional biotype filter (e.g. protein_coding, lncRNA, SNV). Case-sensitive (lncRNA, not lncrna); remove the filter to inspect all matching feature types. Applied server-side by Ensembl. Not all fea...

featurearray

Feature types to retrieve — at least one. Default is gene only. Requesting variation in a large region can match tens of thousands of features. Include variation only for targeted small regions (si...

max_resultsinteger

Maximum number of features to return. A gene-length region can hold tens of thousands of variation features; the default keeps the response compact. Set to 0 to return every feature uncapped. total...default: 100

region*string

Genomic region as chr:start-end with species set (e.g. 13:32315086-32400268), or species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268), with start at or below end. Ensembl serves at most 5...

speciesstring

Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Required for a bare chr:start-end region; for the species:chr:start-end form the species in region takes precedence and this fi...

ensembl_predict_variantPredict 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/a...5 params

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/a...

Parameters* required

include_all_colocated_pubmedboolean

When true, return every PubMed ID for each colocated variant, overriding max_pubmed_ids_per_variant. Default false to keep responses compact.default: false

max_pubmed_ids_per_variantinteger

Maximum PubMed IDs to return per colocated known variant. Well-studied variants (e.g. rs334) cite 100+ papers; the default trims each list. Set to 0 to return every PubMed ID uncapped. pubmedTotal...default: 10

max_transcript_consequencesinteger

Maximum transcript consequences to return per VEP record. High-impact variants can affect 60+ transcripts; the default keeps the response focused on the top consequences. Set to 0 to return every t...default: 10

speciesstring

Species in Ensembl internal format. Default is homo_sapiens. For non-human variants, set the appropriate species (e.g. mus_musculus for mouse). Use ensembl_list_species with nameContains (a genus o...default: homo_sapiens

variant*string

Variant in one of three formats: (1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; genomic: 13:g.32316462T>A; (2) Region+allele: chr:start:end:strand/allele — e.g. 1:65568:65568:1/...

ensembl_get_homologyFind 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), an...6 params

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), an...

Parameters* required

idstring

Ensembl stable gene ID (e.g. ENSG00000139618). A version suffix (ENSG00000139618.17) is accepted and dropped before the query. Use ensembl_lookup_gene to get the stable ID from a symbol. Cannot be...

max_resultsinteger

Maximum number of homologs to return. Broad orthology queries (e.g. BRCA2 across all species) can return 150+ homologs; the default keeps responses focused. Set to 0 to return every homolog uncappe...default: 25

speciesstring

Source species (the species the query gene belongs to) in Ensembl internal format. Default is homo_sapiens. Use ensembl_list_species with nameContains (a genus or common name, e.g. mouse) to find v...default: homo_sapiens

symbolstring

Gene symbol in the source species (e.g. BRCA2, TP53). Species defaults to homo_sapiens; set species for other organisms. Cannot be combined with id.

target_speciesstring

Filter to homologs in a single target species (e.g. mus_musculus for mouse). Omit to return homologs across all available species. Use ensembl_list_species with nameContains (a genus or common name...

typestring

Type of homologs to return. orthologues: genes related by speciation (cross-species equivalents). paralogues: genes related by duplication (within or across species). all: both orthologs and paralogs.one of orthologues · paralogues · alldefault: orthologues

ensembl_get_xrefsRetrieve 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...3 params

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...

Parameters* required

all_levelsboolean

Include references on child objects: a gene includes its transcripts and translations. Default false queries only the requested object level, independently of dbname.default: false

dbnamestring

Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), Uniprot/SWISSPROT (reviewed UniProt accession, on the translation...

id*string

Ensembl stable gene (ENSG…), transcript (ENST…), or translation (ENSP…) ID. A version suffix on an ENS… ID (ENSG00000139618.17) is dropped before the request. Use ensembl_lookup_gene to get the sta...

Configuration

ENSEMBL_BASE_URLdefault: https://rest.ensembl.org

Ensembl REST API base URL. Override to use GRCh37 endpoint or a local mirror.

MCP_LOG_LEVELdefault: info

Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').

MCP_TRANSPORT_TYPEdefault: http

Selects the HTTP transport.

MCP_HTTP_HOSTdefault: 127.0.0.1

The hostname for the HTTP server.

MCP_HTTP_PORTdefault: 3010

The port to run the HTTP server on.

MCP_HTTP_ENDPOINT_PATHdefault: /mcp

The endpoint path for the MCP server.

MCP_AUTH_MODEdefault: none

Authentication mode to use: 'none', 'jwt', or 'oauth'.

Readme

@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

View the full README on GitHub

Details

Repository: github.com/cyanheads/ensembl-mcp-server
Category: Databases
Package: @cyanheads/ensembl-mcp-server
Transport: STDIO, HTTP
Registry: MCP registry, active
Resources: 10
Prompts: 1
Tools verified: Nov 6, 2026

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Ensembl Mcp Server

Install

Tools

Configuration

Readme

@cyanheads/ensembl-mcp-server

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