Ensembl MCP Server vs Genomics MCP
A side-by-side look at the Ensembl MCP Server and Genomics MCP 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 as a local process; choose Genomics MCP 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.
- You prefer a local stdio subprocess transport.
- You want tools like
ensembl_list_species, ensembl_lookup_gene, ensembl_get_sequence.
Choose Genomics MCP when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
list_sources, search_datasets, describe_dataset.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 57/100 · Good | 59/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | Not declared | Not declared |
| Pricing | Not declared | Not declared |
| Required env vars | None listed | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 3 | 3 |
| Directory activity | 1 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 7 | 23 |
| Full listing | View Ensembl MCP Server | View Genomics MCP |
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
Genomics MCP tools 23
list_sourcesList data and reference sources, their state and supported operations.search_datasetsSearch one archive/catalog for studies or datasets by text query. Available for: ega, ena, encode, geo, ncbi_datasets.describe_datasetDescribe a study/dataset by native accession, with linked entities. Available for: ega, ena, encode, geo, ncbi_datasets.list_filesList files of a study/dataset with format, size, checksums, index and readiness. Available for: ega, ena, encode, geo, local, ncbi_datasets, s3.list_samplesList samples of a study/dataset as supplied by the source. Available for: ega, ena, encode, geo, ncbi_datasets.get_sample_metadataGet one sample's metadata and phenotype values exactly as supplied by the source. Available for: ega, ena, encode, geo, ncbi_datasets.fetch_fileStart a bounded download of a file (and index) to the local work dir. Returns a transfer job; files above the default limit need budget_bytes. Available for: default.get_transfer_statusGet progress/result of a transfer started by fetch_file. Available for: default.cancel_transferCancel a running transfer. Available for: default.get_readsAlignments overlapping an interval from indexed BAM/CRAM. Flag filters follow samtools -f/-F. CRAM needs a matching reference unless self-contained. Available for: bam, cram.get_coverageRead depth over an interval from indexed BAM/CRAM (default excludes UNMAP, SECONDARY, QCFAIL, DUP, like samtools depth). Available for: bam, cram.get_pileupPer-position base counts over an interval from indexed BAM/CRAM. Available for: bam, cram.- +11 more on 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
{
"mcpServers": {
"ensembl-mcp-server": {
"command": "bunx",
"args": [
"@cyanheads/ensembl-mcp-server@latest"
]
}
}
}
Genomics MCP
{
"mcpServers": {
"genomics-mcp": {
"command": "uvx",
"args": [
"rewire-genomics-mcp"
]
}
}
}
Frequently asked questions
Ensembl MCP Server is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Genomics MCP belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick Ensembl MCP Server for biology & bioinformatics work and Genomics MCP 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 declared pricing — check the project's own site. Genomics MCP 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 genomics-mcp 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 57/100 (Good) with 1 views, 0 installs and 3 GitHub stars. Genomics MCP has 59/100 (Good) with 1 views, 0 installs and 3 GitHub stars.