BioMCP TS vs Gnomad Genetics MCP Server
A side-by-side look at the BioMCP TS and Gnomad Genetics MCP Server MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose BioMCP TS for biology & bioinformatics work as a local process; choose Gnomad Genetics MCP Server 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 BioMCP TS when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You want tools like
gene_search, gene_get, gene_diseases.
Choose Gnomad Genetics MCP Server when
- You need dedicated capabilities in the Biology & Bioinformatics domain.
- You prefer a local stdio subprocess transport.
- You have the keys it needs:
GNOMAD_DATAFRAME_DROP_ENABLED, GNOMAD_MAX_VARIANT_BATCH. - You want tools like
gnomad_get_variant, gnomad_get_gene_constraint, gnomad_list_gene_variants.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Biology & Bioinformatics | Biology & Bioinformatics |
| Quality signal | 59/100 · Good | 56/100 · 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 | GNOMAD_DATAFRAME_DROP_ENABLEDGNOMAD_MAX_VARIANT_BATCH |
| Verified owner | Community listing | Community listing |
| GitHub stars | 12 | 1 |
| Directory activity | 1 views 0 installs 0 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 53 | 8 |
| Full listing | View BioMCP TS | View Gnomad Genetics MCP Server |
Tools & capabilities
BioMCP TS tools 53
gene_searchSearch genes by symbol, name, or keyword with chromosome filtergene_getGet detailed gene info by HGNC symbol with optional sections (core, pathways, protein, ontology, go, interactions, expression, protein_atlas, constraint, druggability, dosage_sensitivity, clinical_evidence, disease_associations, diseases, funding). Set `smart=true` to auto-resolve gene aliases (e.g…gene_diseasesGet diseases associated with a gene (DisGeNET / OpenTargets)gene_drugsFind drugs targeting a gene (OpenTargets)gene_trialsFind clinical trials for a genegene_articlesFind articles about a gene (federated across PubMed, EuropePMC, Semantic Scholar, arXiv, PubTator, LitSense; envelope `{ results, warnings?, errors? }` — per-backend failures ride in `errors`)gene_enrichPathway enrichment analysis for a gene list (Reactome)variant_searchSearch variants by rsid, HGVS, gene, ClinVar significance, frequency, CADDvariant_getGet detailed variant info with optional sections (frequency, predictions, clinical; `alphagenome_scores` currently returns an unavailability error pending reimplementation)variant_oncokbGet OncoKB cancer variant annotations (requires `ONCOKB_TOKEN`)variant_trialsFind clinical trials for a variantdrug_searchSearch drugs by name, mechanism, or keyword (envelope `{ results, hint? }` — when nothing matches, `hint` points mechanism/target queries at gene_drugs)- +41 more on the listing page
Gnomad Genetics MCP Server tools 8
gnomad_get_variantFull population record for one or more variants — AC/AN/AF overall and per genetic-ancestry group, homozygote/hemizygote counts, quality flags, transcript consequence, in-silico predictors, and joined ClinVar significance.gnomad_get_gene_constraintGene loss-of-function constraint — pLI, LOEUF (`oe_lof_upper`) with confidence interval, observed/expected ratios, and Z-scores. By HGNC symbol or Ensembl gene ID.gnomad_list_gene_variantsEvery variant in a gene, transcript, or region with allele frequencies and predicted consequences, filterable by consequence class and max allele frequency.gnomad_get_coverageSequencing coverage across a gene, transcript, or region — mean/median depth and the fraction of samples over depth thresholds, per callset track.gnomad_search_clinvarGene-level ClinVar detail via NCBI E-utilities — classified variants, review status, conditions, submission counts, and gnomAD-compatible variant IDs, paged by offset.gnomad_dataframe_queryRun a read-only SQL `SELECT` across canvas tables staged by the list tools.gnomad_dataframe_describeList the tables staged on a canvas and their columns before writing SQL.gnomad_dataframe_dropDrop a named table from a canvas to reclaim memory. Opt-in via `GNOMAD_DATAFRAME_DROP_ENABLED=true` — off by default.
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.
BioMCP TS
{
"mcpServers": {
"biomcp-ts": {
"command": "npx",
"args": [
"-y",
"biomcp"
]
}
}
}
Gnomad Genetics MCP Server
{
"mcpServers": {
"gnomad-genetics-mcp-server": {
"command": "bunx",
"args": [
"@cyanheads/gnomad-genetics-mcp-server@latest"
],
"env": {
"GNOMAD_DATAFRAME_DROP_ENABLED": "YOUR_GNOMAD_DATAFRAME_DROP_ENABLED_HERE",
"GNOMAD_MAX_VARIANT_BATCH": "YOUR_GNOMAD_MAX_VARIANT_BATCH_HERE"
}
}
}
}
Frequently asked questions
BioMCP TS is categorized under Biology & Bioinformatics and uses a local stdio subprocess. Gnomad Genetics MCP Server belongs to Biology & Bioinformatics and uses a local stdio subprocess. Pick BioMCP TS for biology & bioinformatics work and Gnomad Genetics MCP Server 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.
BioMCP TS has no declared pricing — check the project's own site. Gnomad Genetics MCP Server 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 biomcp-ts and gnomad-genetics-mcp-server as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, BioMCP TS has a quality signal of 59/100 (Good) with 1 views, 0 installs and 12 GitHub stars. Gnomad Genetics MCP Server has 56/100 (Good) with 1 views, 0 installs and 1 GitHub stars.