Ensembl MCP. Run advanced genomic queries from natural conversation.
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Ensembl connects to the Ensembl REST API, letting your AI agent access complex genomic data. You can pull gene trees, find homologies across species, check variant consequences (VEP), and map coordinates between assemblies.
It's for advanced bioinformaticians who need to run complex queries—like cross-referencing an ID to an external symbol—without writing custom R or Python scripts.
What your AI agents can do
Get alignment
Retrieves genomic alignments for a specific region.
Get archive bulk
Gets the latest version for a set of identifiers.
Get archive id
Returns the latest version of a single identifier.
The agent retrieves gene trees and homology data for stable identifiers, showing how genes relate across different species.
The agent predicts the biological impact of a genetic variant using tools like get_vep_hgvs or get_vep_id.
The agent finds external identifiers linked to an Ensembl object using symbols or specific IDs, such as running get_xrefs_symbol.
The agent converts coordinate systems (e.g., cDNA to genomic) using tools like get_map or get_map_cdna.
The agent lists available species or retrieves specific assembly information for a given species using get_info_species.
The agent processes multiple identifiers or regions at once using bulk tools like get_lookup_bulk or get_vep_bulk.
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Ensembl MCP Server: 27 Tools for Genomic Data Analysis
Analyze alignments, retrieve gene trees, and calculate LD values by using these 27 specialized tools through a natural conversation.
019e5d16get alignment
Retrieves genomic alignments for a specific region.
019e5d16get archive bulk
Gets the latest version for a set of identifiers.
019e5d16get archive id
Returns the latest version of a single identifier.
019e5d16get ga4gh beacon
Provides allele information using the Beacon service.
019e5d16get genetree
Retrieves a gene tree for a stable identifier.
019e5d16get homology
Gets homology information based on species and gene ID.
019e5d16get info assembly
Lists available assemblies and chromosomes for a specific species.
019e5d16get info rest
Checks the current version of the Ensembl REST API.
019e5d16get info species
Lists all available species and their metadata.
019e5d16get ld
Computes Linkage Disequilibrium (LD) values.
019e5d16get lookup bulk
Performs a bulk lookup for multiple identifiers.
019e5d16get lookup id
Finds the species and database for a single identifier.
019e5d16get map
Converts coordinates from one assembly version to another.
019e5d16get map cdna
Converts cDNA coordinates to genomic coordinates.
019e5d16get ontology id
Searches for an ontological term by its identifier.
019e5d16get overlap region
Retrieves features that overlap a specific genomic region.
019e5d16get sequence id
Requests a genomic sequence using a stable identifier.
019e5d16get sequence region
Requests a genomic sequence defined by a specific region.
019e5d16get taxonomy id
Searches for a taxonomic term by ID or name.
019e5d16get variation
Retrieves variant features, genotypes, and population data.
019e5d16get vep bulk
Performs consequence prediction for multiple genomic regions.
019e5d16get vep hgvs
Fetches consequences for a variant using HGVS notation.
019e5d16get vep id
Fetches consequences for a variant using an ID (e.g., rsID).
019e5d16get xrefs id
Retrieves external references for a given Ensembl identifier.
019e5d16get xrefs symbol
Looks up an external symbol and returns all linked Ensembl objects.
019e5d16ping
Checks if the server connection is active.
019e5d16search ga4gh variants
Searches for genetic variants using the GA4GH schema.
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What you can do with this MCP connector
Yo, this Ensembl MCP Server hooks up your AI agent straight to the Ensembl REST API. You can pull complex genomic data without writing a single line of R or Python. You'll use it when you need to run deep bioinfo queries—like tracing gene family relationships or checking variant consequences—just by talking to your agent.
Gene Relationships and Comparative Genomics
get_genetree: Retrieves a gene tree for any stable identifier.get_homology: Gets homology information based on species and gene ID, letting you trace how genes relate across different species.get_info_species: Lists every species available and their metadata.get_info_assembly: Shows available assemblies and chromosomes for a specific species.get_sequence_id: Requests a genomic sequence using a stable identifier.get_sequence_region: Requests a genomic sequence defined by a specific region.get_alignment: Retrieves genomic alignments for a specific region.
Variant and Sequence Analysis
get_vep_id: Fetches the biological consequences for a variant using an ID, like an rsID.get_vep_hgvs: Predicts consequences for a variant using HGVS notation.get_vep_bulk: Runs consequence prediction for multiple genomic regions at once.get_variation: Retrieves variant features, genotypes, and population data.get_ga4gh_beacon: Provides allele information using the Beacon service.search_ga4gh_variants: Searches for genetic variants using the GA4GH schema.get_overlap_region: Finds features that overlap a specific genomic region.
Mapping and Coordinate Conversion
get_map: Converts coordinates from one assembly version to another.get_map_cdna: Converts cDNA coordinates to genomic coordinates, which is crucial for analysis.
Lookups, Cross-Referencing, and Archiving
get_xrefs_symbol: Looks up an external symbol (like BRCA2) and returns all linked Ensembl objects.get_xrefs_id: Retrieves external references for a given Ensembl identifier.get_lookup_id: Finds the species and database for a single identifier.get_lookup_bulk: Performs a bulk lookup for multiple identifiers.get_archive_id: Returns the latest version of a single identifier.get_archive_bulk: Gets the latest version for a set of identifiers.get_info_rest: Checks the current version of the Ensembl REST API.get_taxonomy_id: Searches for a taxonomic term by ID or name.get_ontology_id: Searches for an ontological term by its identifier.get_ld: Computes Linkage Disequilibrium (LD) values.get_overlap_region: Retrieves features that overlap a specific genomic region.
How Ensembl MCP Works
- 1 Subscribe to the Ensembl server and configure your API key. You can use 'PUBLIC' for standard access.
- 2 Ask your AI client to perform a query. For example: 'What is the homology for ENSG00000139618 in mouse?'
- 3 The agent executes the necessary tools (like
get_homology) and returns the structured genomic data directly to your chat environment.
The bottom line is that you get structured, complex genomic data—like alignments and homology—without ever writing a single line of R or Python code.
Who Is Ensembl MCP For?
This is for bioinformaticians and genomic researchers who need to pull highly specific data without the friction of writing custom scripts. If your job involves comparing genes across species, checking variant types, or mapping coordinates, this saves hours of manual scripting.
Uses the server to pull gene trees and homology data, automating complex comparisons that used to require multiple scripts.
Verifies stable ID versions or cross-references symbols (like BRCA2) directly within their research environment.
Automates the retrieval of genomic alignments and metadata for large-scale biological analysis, especially using bulk tools.
What Changes When You Connect
- Get homology data and gene trees instantly. Instead of running separate scripts for
get_homologyandget_genetree, your agent handles the complex, multi-species comparisons in one query. - Handle large datasets with bulk tools. Use
get_vep_bulkorget_lookup_bulkto process hundreds of identifiers or regions at once, eliminating the need for slow, iterative API calls. - Translate coordinates easily. If you get cDNA data, use
get_map_cdnato get the genomic coordinates needed for downstream analysis, saving manual conversion steps. - Cross-reference IDs quickly. Use
get_xrefs_symbolto look up a known gene symbol (like BRCA2) and immediately get every linked Ensembl ID, saving time finding the correct accession number. - Analyze variants with specific inputs. You don't just get a list of variants; you can run
get_vep_hgvsorget_vep_idto predict the functional consequence of a variant using specific notations. - Manage metadata and species info. Use
get_info_speciesto list all available species and check their specific assembly details before running a major comparative analysis.
Real-World Use Cases
Comparing Human and Mouse Genes
A researcher needs to find all orthologs for a human gene (ENSG...) in mouse. They ask their agent, which then executes get_homology and returns a list of high-confidence orthologues, along with the necessary accession numbers for follow-up analysis.
Validating a Research ID
A data scientist finds a new variant ID (rsID) and needs to know its current status. They ask the agent, which uses get_vep_id to fetch the predicted consequence and the correct database information, immediately confirming if the ID is stable.
Mapping Coordinates for a New Assay
A wet-lab biologist gets sequencing data with cDNA coordinates. They ask the agent to convert these coordinates to genomic coordinates using get_map_cdna. This makes the data usable for downstream alignment tools.
Large-Scale Database Audit
A bioinformatician needs to check the current version and metadata for 50 different genes. Instead of 50 individual calls, they use get_archive_bulk, which processes the entire list efficiently and returns the latest stable version for every item.
The Tradeoffs
Sequential ID lookups
Looking up the latest version of 50 identifiers one by one using get_archive_id in a loop. This is slow, wastes API quota, and is prone to timeouts.
→
Use get_archive_bulk instead. It processes all 50 identifiers in a single, efficient call, giving you the latest version metadata for the entire batch.
Ignoring specialized inputs
Trying to run a variant query without knowing the exact input format, leading to vague or unusable results.
→
Use the specific tools: If you have HGVS notation, use get_vep_hgvs. If you have an rsID, use get_vep_id. The server handles the correct input structure.
Copying and pasting regions
Manually converting coordinates from a spreadsheet into the API call for get_map or get_map_cdna, which is tedious and error-prone.
→
Just ask the agent. 'Convert these coordinates from assembly X to assembly Y.' The agent handles the mapping logic using get_map and get_map_cdna.
When It Fits, When It Doesn't
Use this server if your work requires comparing genes across species, predicting variant consequences, or dealing with coordinate systems. It's best for bioinformaticians who need to run complex, multi-step analyses (e.g., find homology, then predict VEP consequences). Don't use this if you only need basic API status checks or simple data lookups that don't require complex biological mapping. If you only need to list species, get_info_species is sufficient, but for anything involving relations (like homology or mapping), use the full suite.
Independent Platform Disclaimer: Vinkius is an independent platform and is not affiliated with, endorsed by, sponsored by, verified by, or otherwise authorized by Ensembl. All third-party trademarks, logos, and brand names are the property of their respective owners. Their use on this website is strictly for informational purposes to identify service compatibility and interoperability.
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Works with Claude, ChatGPT, Cursor, and more
The Model Context Protocol standardizes how applications expose capabilities to LLMs. Instead of operating in isolation, your AI gains direct access to external platforms, live data, and real-world actions through secure, standardized connections.
This server provides 27 capabilities that interface natively with Claude, ChatGPT, Cursor, and any MCP client. No middleware. No custom integration required.
Available Capabilities
Manually cross-referencing identifiers across different databases is a massive time sink.
Finding the correct, stable ID for a gene—especially when you're dealing with multiple species or different assemblies—is painful. You have to check NCBI, then Ensembl, then BLAST, manually updating the ID every time the database version changes. It's a cycle of copy/paste and manual verification.
With the Ensembl MCP Server, you simply ask: 'What is the latest stable ID for this gene?' The agent runs `get_archive_id` and gives you the current, correct accession number immediately. You get reliable data, not manual guesswork.
Ensembl MCP Server: Link a gene symbol to all known records.
Previously, if you knew a gene symbol like BRCA2, you had to search multiple portals to find the corresponding Ensembl accession numbers. This meant opening three different tabs and manually copying multiple IDs.
Now, you ask the agent to look up the symbol using `get_xrefs_symbol`. It instantly returns all linked Ensembl objects and cross-references, consolidating what used to take minutes of searching into a single, conversational query.
Common Questions About Ensembl MCP
How do I find the latest version of an Ensembl ID using get_archive_id? +
Use get_archive_id to get the current metadata. You just provide the identifier, and the server returns the latest stable version and assembly information.
Can get_homology handle multiple species comparisons? +
Yes, get_homology is designed to retrieve homology information across specified species and gene IDs, making comparative genomics straightforward.
What is the difference between get_vep_hgvs and get_vep_id? +
They handle different inputs. Use get_vep_hgvs when you have the full HGVS notation for a variant. Use get_vep_id when you have a standard identifier like an rsID.
Does get_map_cdna convert coordinates reliably? +
Yes, get_map_cdna converts cDNA coordinates to genomic coordinates, which is vital for translating raw sequencing reads into a usable format.
What is the best way to cross-reference a gene symbol? +
Use get_xrefs_symbol. This tool takes a symbol (e.g., BRCA2) and returns all associated Ensembl objects, linking the symbol to the entire database.
How do I use get_info_species to list all available species? +
You simply call get_info_species with no arguments. This returns a list of all species supported by the database. You can then filter this list to focus on the taxa relevant to your study.
What's the best way to check for overlapping regions using get_overlap_region? +
The get_overlap_region tool takes a region and a list of features. It returns all features that overlap that specific genomic area. This is useful for seeing what data falls into a defined spot.
If I run get_lookup_bulk, how do I handle identifiers that might be invalid? +
The get_lookup_bulk function processes a list of identifiers and returns the status for each one. Invalid IDs will return a specific error structure, allowing your agent to skip them and continue processing the rest of your batch.
How can I find orthologs for a specific gene across different species? +
Use the get_homology tool by providing the species name and the Ensembl gene ID. You can filter by type (e.g., 'orthologues') to see related genes in other organisms.
Can I retrieve the evolutionary gene tree for a specific identifier? +
Yes! The get_genetree tool allows you to fetch the gene tree for any stable Ensembl ID, with options for alignment and sequence types (protein or cdna).
How do I map a common gene symbol like 'BRCA2' to its Ensembl ID? +
Use the get_xrefs_symbol tool. Provide the species (e.g., 'human') and the symbol 'BRCA2' to retrieve all linked Ensembl objects and their stable identifiers.
Use it with your favorite AI tools
Connect this server to Cursor, Claude, VS Code, and more.
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