# Ensembl MCP for AI Agents AI Agent Connect > Ensembl MCP for AI Agents. Access genomic data, gene trees, and homologies from the Ensembl database directly from any AI agent. ## Overview - **Category:** databases - **Price:** Free - **Endpoint:** https://edge.vinkius.com/vk_preview_m0hayIErvjxLYR70lCwlpWpppEzV8unFkuPlELTW/ai-agent-connect - **Tags:** genomics, bioinformatics, gene-trees, dna-sequencing, biological-data ## Description The Ensembl MCP lets you pull advanced genomic data and biological records directly into your AI client. You can ask your agent to find specific gene trees, look up homologies like orthologs and paralogs, or grab genomic alignments across multiple species. It handles the heavy lifting of interacting with the Ensembl REST API so you don't have to write custom Python or R scripts to get your data. If you need to find the latest stable identifiers for a set of genes, or if you need to map coordinates from one assembly version to another, this Connector handles those requests in seconds. It also provides access to variant effect prediction, which is huge for understanding how mutations actually impact biology. You can even use it to list all available species or search for specific ontological terms and taxonomic IDs. It makes it easy to bridge the gap between raw database records and your actual research. Using this Connector through the Vinkius catalog means you get a reliable way to turn natural language questions into precise genomic data. Instead of toggling between tabs and copying IDs, your agent can fetch exactly what you need for your analysis. This means you spend less time on data entry and more time on the actual science. Whether you're looking for a specific mutation's consequence or a broad overview of a species' genome, the data is just a prompt away. ## Tools ### get_info_assembly Lists the available assemblies and chromosomes for a species. This helps you understand the structural layout of a genome. ### get_info_rest Shows the current version of the Ensembl REST API. Use this to check for the latest updates to the service. ### get_info_species Lists all available species and their metadata. This is the best way to see what organisms are in the database. ### get_vep_id Fetches consequences for a variant identifier like an rsID. This is the easiest way to check a known SNP's impact. ### get_xrefs_id Retrieves external references for an Ensembl identifier. This helps you link your data to other major databases. ### get_xrefs_symbol Looks up an external symbol and returns linked Ensembl objects. Use this to find the correct Ensembl ID from a common gene name. ### get_alignment Retrieves genomic alignments for a specific region. This helps you see how sequences line up across different species. ### get_archive_bulk Returns the latest versions for a group of identifiers. Use this to quickly update a large list of gene IDs. ### get_archive_id Finds the latest version of a single identifier. This ensures you're always working with the most current data. ### get_ga4gh_beacon Provides allele information through a beacon service. This is great for checking specific genetic markers. ### search_ga4gh_variants Searches for variants using the GA4GH schema. Use this to query specific genetic variations in your research. ### get_genetree Retrieves a gene tree for a stable identifier. It helps you visualize the evolutionary relationships of a gene. ### get_homology Pulls homology information by species and gene ID. Use this to find orthologs and paralogs across different organisms. ### get_ld Computes Linkage Disequilibrium values. This is essential for understanding how genetic markers are inherited together. ### get_lookup_bulk Performs a bulk lookup for multiple identifiers. Use this to quickly find the database and species for a list of IDs. ### get_lookup_id Finds the species and database for a single identifier. This is helpful when you have an ID but don't know its origin. ### get_map_cdna Converts cDNA coordinates to genomic coordinates. This helps you translate transcript data into genome locations. ### get_map Converts coordinates from one assembly version to another. This is a lifesaver when moving between older and newer genome versions. ### get_ontology_id Searches for an ontological term by its identifier. Use this to link your data to standard biological terms. ### get_overlap_region Retrieves features that overlap a specific region. This helps you see what genes or markers are in a specific area. ### ping Checks if the service is currently alive. Use this to verify your connection to the Ensembl API. ### get_sequence_id Requests a sequence by its stable identifier. This gives you the raw data for a specific gene or transcript. ### get_sequence_region Requests a genomic sequence by a specific region. Use this to pull a specific piece of DNA for analysis. ### get_taxonomy_id Searches for a taxonomic term by ID or name. This helps you categorize species and organisms correctly. ### get_variation Retrieves variant features, genotypes, and population data. Use this to see how specific mutations occur in populations. ### get_vep_bulk Provides consequence predictions for multiple regions. This is the fastest way to see the impact of several variants at once. ### get_vep_hgvs Fetches consequences for a variant in HGVS notation. Use this when you need to understand a specific mutation's effect. ## Prompt Examples **Prompt:** ``` What is the latest version of the Ensembl identifier ENSG00000139618? ``` **Response:** ``` I've checked the archive for ENSG00000139618. The latest version is **version 11**, which is currently active in the latest assembly. ``` **Prompt:** ``` Find all orthologues for the human gene ENSG00000139618 in mouse. ``` **Response:** ``` Searching homologies... I found **1 high-confidence orthologue** in *Mus musculus*: **ENSMUSG00000041147 (Brca2)**. Would you like the alignment details? ``` **Prompt:** ``` List all species currently available in the Ensembl database. ``` **Response:** ``` I've retrieved the species list. There are **over 300 species** available, including: * *Homo sapiens* * *Mus musculus* * *Danio rerio* Would you like me to filter this list by a specific taxon? ``` ## Capabilities ### Fetch gene trees Retrieve evolutionary relationships for specific gene identifiers. ### Find orthologues Identify homologous genes across different species instantly. ### Map genomic coordinates Convert coordinates between different assembly versions easily. ### Predict variant effects Get biological consequence data for specific genetic mutations. ### Bulk ID lookups Retrieve metadata for large sets of identifiers in one go. ## Use Cases ### Comparative Genomics Analysis A researcher asks their agent to find all orthologues for a human gene in mouse. The agent uses get_homology to find the match and pull the sequence. ### Variant Impact Assessment A clinician needs to know the effect of a specific rsID. They ask the agent to check the variant impact, and it uses get_vep_id to return the consequences. ### Cross-Assembly Mapping A scientist is moving data from an old genome build to a new one. They ask the agent to convert a list of coordinates using get_map. ### Rapid Species Discovery A student wants to see which organisms are covered in the database. They ask the agent to list all species, and it returns a full metadata list. ## Benefits - Skip writing custom scripts by using get_genetree to pull evolutionary data instantly. - Save hours of manual searching with get_homology to find orthologues across species. - Maintain data integrity with get_archive_id to always pull the latest stable identifiers. - Simplify cross-assembly analysis by using get_map to convert coordinates between versions. - Get immediate biological context for mutations with get_vep_id and get_vep_hgvs. - Bulk process your research data with get_lookup_bulk to handle hundreds of IDs in one request. ## How It Works The bottom line is you get direct, conversational access to the Ensembl database without writing any code. 1. Subscribe to the Ensembl MCP and add it to your AI client. 2. Enter your API configuration, using 'PUBLIC' for standard access. 3. Ask your agent to pull gene trees, sequences, or variant data. ## Frequently Asked Questions **Can the Ensembl MCP find orthologues for me?** Yes, it can find orthologues across different species. You can simply ask your agent to find the matches for a specific gene, and it will pull the homology data for you. **How do I get genomic sequences with Ensembl MCP?** You can request sequences by their stable identifier or by a specific region. Your agent will fetch the raw genomic data directly from the Ensembl database. **Can I use Ensembl MCP for variant analysis?** Yes, it provides access to variant effect prediction. You can ask about specific mutations to see how they impact biology or get consequences for a list of regions. **Does Ensembl MCP support multiple species?** It supports over 300 species. You can list the available species or query specific metadata for any of them through your AI client. **Can I map coordinates between different assemblies?** Yes, the Connector includes a tool to convert coordinates from one assembly version to another. This is very helpful when working with older and newer genome builds. **Is the Ensembl MCP good for large-scale data pulls?** It's great for bulk lookups. You can provide a list of identifiers, and the agent can retrieve the latest versions and metadata for all of them in one go. **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.