MCP server that wraps the Dagster GraphQL API — manage runs, assets, schedules, sensors, and backfills from any MCP client
Nothing to run from here
Ensembl Genomics is installed from its publisher's own source and answers where it runs, so this marketplace is not in the path of a single call. There is no address here to send one to, and a panel that pretended otherwise would be showing you an answer we made up. Install it and call it from your own client — the Installation tab has the entry for each one.
7
tools declared
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trust score
remote
at its publisher
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calls last 7d
What it does
Look up genes, fetch sequences, predict variant consequences and find orthologs via Ensembl REST.
Quickstart
# 1 — add it to Claude Code
claude mcp add --scope user --transport http ensembl-genomics-mcp https://ensembl.caseyjhand.com/mcp
# 2 — ask your agent for something these tools do
# ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence and 4 more
Ensembl Genomics costs nothing on mcprush: there is no plan to choose here, no cap to set and nothing mcprush can bill you for.
Publishernot claimed
ECAll 1 server
ensembl.caseyjhand.com1 server
1 category
Collected from a public index. Nobody has claimed this account, so nothing here was written by its author — claim it if it is yours.
Installation
Where are you running it?
Every route below installs the same thing and ends at the same approval screen. Nothing here runs on your machine and nothing runs on ours: this server answers at its publisher’s own address, and what you install is the connection straight to it.
Claude Codedeclared by this listing
This is a public server: it answers at its publisher’s own address and this marketplace is not in the path. Claude Code registers it in one command; --scope user makes it available in every project. The transport below is http, as the publisher's own manifest declares it.
claude mcp add --scope user --transport http ensembl-genomics-mcp https://ensembl.caseyjhand.com/mcpReconnect, or start a new session, and the tools appear in the model’s tool list.
Free on mcprush, and it answers at its publisher’s own address: this marketplace is not in the path, so there is no key of ours to hold and no card to add.
What it writes
One config entry pointing straight at the publisher’s own address — this marketplace is not in the path, and nothing from this listing executes on your machine.
What you approve
7 tools, with what each one reads, writes and reaches shown before you agree — the same list on every route above. Read the tool surface.
Tool surface
What the model actually sees. Descriptions are diffed on every release — see version history.
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. Filter by division to select one; use nameContains to find a species by partial name match. With no division, returns the endpoint default division — the
| Parameter | Type | Required | Notes |
|---|---|---|---|
| division | string | no | Filter to a specific Ensembl division. EnsemblVertebrates includes human, mouse, zebrafish, and other vertebrates. EnsemblPlants covers crop and model plant genomes. EnsemblFungi, EnsemblMetazoa, Ense |
| nameContains | string | no | 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. |
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 lookup (BRCA2 + homo_sapiens) and direct ID lookup (ENSG00000139618). Supports batch lookup of up to 20 IDs or symbols i
| Parameter | Type | Required | Notes |
|---|---|---|---|
| symbol | string | no | 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. |
| id | string | no | Ensembl stable gene ID (e.g. ENSG00000139618 or ENSG00000139618.7 with version). Species is not required for ID lookup. |
| species | string | no | 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 other |
| ids | array | no | Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols. |
| symbols | array | no | Batch lookup: up to 20 gene symbols. Species defaults to homo_sapiens; set species for other organisms. Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols. |
| expand_transcripts | boolean | no | 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. |
Fetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic region. Returns the sequence with its stable ID, molecule type, and character count — large sequences are returned in full but the length is stated so callers can budget context. The type parameter selects which sequence is fetched: genomic (default, includes introns), cdna (spliced transcript), cds (coding s
| Parameter | Type | Required | Notes |
|---|---|---|---|
| id | string | yes | Ensembl stable ID (ENSG…, ENST…, ENSP…) or a genomic region for region mode. Region accepts species:chr:start-end (e.g. homo_sapiens:13:32315086-32400268) or a bare chr:start-end (e.g. 13:32315086-324 |
| type | string | no | 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 codi |
| species | string | no | Species in Ensembl internal format (e.g. homo_sapiens). Required for a bare chr:start-end region; optional for the species:chr:start-end form (the embedded species is used when the field is omitted). |
| expand_5prime | integer | no | Number of base pairs to extend upstream (5' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries. |
| expand_3prime | integer | no | Number of base pairs to extend downstream (3' direction) of the requested feature. Default 0. Only applies to genomic sequences and region queries. |
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. Useful for "what's in this locus?" and for seeding follow-up lookups. Region format is chr:start-end (e.g. 13:32315086-32400268 for the BRCA2 locus). Ensembl normalizes chromosome names and canonical vertebr
| Parameter | Type | Required | Notes |
|---|---|---|---|
| species | string | yes | Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). Use ensembl_list_species to discover valid values. |
| region | string | yes | Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like c |
| feature | array | no | Feature types to retrieve. Default is gene only. Requesting variation in a large region can return tens of thousands of features. Include variation only for targeted small regions (single gene loci or |
| biotype | string | no | Optional biotype filter (e.g. protein_coding, lncRNA, SNV). Applied server-side by Ensembl. Not all feature types support biotype filtering. |
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/allele, e.g. 1:65568:65568:1/T); and a dbSNP rsID (e.g. rs334). Returns the most severe consequence term, affected transcrip
| Parameter | Type | Required | Notes |
|---|---|---|---|
| variant | string | yes | 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/T ( |
| species | string | no | 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 to discover valid values. |
| max_transcript_consequences | integer | no | 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 tran |
| max_pubmed_ids_per_variant | integer | no | 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 on |
| include_all_colocated_pubmed | boolean | no | When true, return every PubMed ID for each colocated variant, overriding max_pubmed_ids_per_variant. Default false to keep responses compact. |
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.), perc_id (percent identity), perc_pos (percent positives), and taxonomy level. Essential for cross-species research — for example, "what is the mouse equivalent of human TP53?" or "how conserved is BRCA2 across mammals?". P
| Parameter | Type | Required | Notes |
|---|---|---|---|
| symbol | string | no | 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. |
| id | string | no | Ensembl stable gene ID (e.g. ENSG00000139618). Use ensembl_lookup_gene to get the stable ID from a symbol. Cannot be combined with symbol. |
| species | string | no | Source species (the species the query gene belongs to) in Ensembl internal format. Default is homo_sapiens. Use ensembl_list_species to discover valid values. |
| target_species | string | no | 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 to discover valid values. |
| type | string | no | 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. |
| max_results | integer | no | 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 uncapped. |
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. The dbname filter narrows to specific databases; omit to return all xrefs. IDs returned here chain to protein (pubchem via UniProt), literature (pubmed via PubMed IDs), disease (OMIM via MIM_GENE
| Parameter | Type | Required | Notes |
|---|---|---|---|
| id | string | yes | Ensembl stable gene ID (ENSG…) or transcript ID (ENST…). Use ensembl_lookup_gene to get the stable ID from a gene symbol. xrefs/id returns the full cross-reference set (56+ entries for well-annotated |
| dbname | string | no | Filter to a specific external database by its Ensembl internal name. Examples: HGNC (HGNC gene ID), Uniprot_gn (UniProt gene name), EntrezGene (NCBI Gene ID), MIM_GENE (OMIM disease gene), RefSeq_mRNA |
Free
$0 forever
- Every tool — any call limit is its publisher’s, not ours
- No card, and mcprush charges nothing for it
- Runs at its publisher’s own address — this marketplace is not in the path
- Nothing to cap, because mcprush bills nothing
What counts against your monthly calls
| Tool | Unit | Calls used | Out of the allowance |
|---|
Nothing here is billable: mcprush charges nothing to install Ensembl Genomics or to call it, at any volume.
Call allowance · this installenforced at the gateway
Monthly allowance, in calls
—
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Alert at 80% · then the tool returns a normal MCP error
Used this month: —
—Grade not published
No rule-by-rule report on file for this release
Two independent axes, because powerful and malicious are different questions. The grade is threat only. The capability level is blast radius, and it is never a penalty on the grade — it is priced as one subtract-only term in the score, where you can see it.
This listing is an address its publisher runs, and you connect to it directly — this marketplace is not in the path. The scanner reads packages and public source, and an address is neither. So there is no grade — not a withheld one, an unmeasured one.
Release history
This is an address its publisher runs: which release it serves is theirs to choose, so there is nothing here to pin. The history below is for reading; the current release on file is 0.4.3.
0.4.3
undated
latestNo release note was published with this version.
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One review per account, from a signed-in account that does not publish this listing. Nothing else is asked — you can say what you think before you install it. Publishers can reply once per review, and a review can be edited or deleted by whoever wrote it.
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