Ensembl MCP Server vs Gtex
A side-by-side look at the Ensembl MCP Server and Gtex MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Ensembl MCP Server for biology & bioinformatics work; choose Gtex for biology & bioinformatics as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Ensembl MCP Server when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- Its auth model fits you: No auth required.
- You want tools like
ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence.
Choose Gtex when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 53/100 · Good | 41/100 · Fair |
| Install command | Not confirmed yet | Confirmed |
| Transport | — | Local subprocess (stdio) |
| Auth | No auth required | Not declared |
| Pricing | Free | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 3 | 0 |
| Directory activity | 1 views 0 installs 0 upvotes | 2 views 0 installs 0 upvotes |
| Tools | 7 | Not listed |
| Full listing | View Ensembl MCP Server | View Gtex |
Tools & capabilities
Ensembl MCP Server tools 7
ensembl_list_speciesList species supported by Ensembl with display name, common name, assembly, taxon ID, and divisionensembl_lookup_geneResolve a gene by symbol (synonyms and former symbols included) + species or by stable ID to its Ensembl ID, genomic location, biotype, and transcript listensembl_get_sequenceFetch the DNA, cDNA, CDS, or protein sequence for a gene, transcript, protein, or genomic regionensembl_query_regionFind genomic features (genes, transcripts, variants, regulatory elements, exons) overlapping a chromosomal regionensembl_predict_variantPredict functional consequences of a sequence variant using the Ensembl Variant Effect Predictor (VEP)ensembl_get_homologyFind orthologs and/or paralogs of a gene across species with percent identity and taxonomy levelensembl_get_xrefsRetrieve cross-database references for a gene — HGNC, UniProt, EntrezGene, OMIM, RefSeq, Reactome, and others
Gtex tools
No tool names declared yet. Check the project README from the listing page.
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Ensembl MCP Server
No confirmed install command for Ensembl MCP Server yet — follow the setup steps linked from its listing page rather than a guessed package name.
Gtex
{
"mcpServers": {
"gtex": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-gtex"
]
}
}
}
Frequently asked questions
Ensembl MCP Server is categorized under Biology & Bioinformatics and uses an install path we have not confirmed yet. Gtex belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Ensembl MCP Server for biology & bioinformatics work and Gtex for biology & bioinformatics.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client. Ensembl MCP Server has no confirmed install command yet — follow its own setup instructions.
Ensembl MCP Server is listed as free. Auth: no auth required. Gtex has no declared pricing — check the project's own site. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add ensembl-mcp-server and gtex as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Ensembl MCP Server has a quality signal of 53/100 (Good) with 1 views, 0 installs and 3 GitHub stars. Gtex has 41/100 (Fair) with 2 views, 0 installs and 0 GitHub stars.