GWAS Bioinformatics MCP Server
This server wraps 14 major bioinformatics databases into 30+ tools you can query through Claude. You get UniProt and Ensembl for gene lookups, ClinVar for variant pathogenicity, STRING for protein interactions, AlphaFold and PDB for structures, KEGG for pathways, Open Targets and PharmGKB for drug discovery, plus GWAS Catalog, GTEx eQTLs, and OMIM disease data. All responses are cached for an hour to keep things fast. Reach for this when you're doing computational biology work and want to pull data from multiple sources without juggling API keys or writing scrapers. The tool names are straightforward: search_uniprot, get_clinvar_variant, get_protein_interactions, search_kegg_pathway.
- GitHub stars
- 1
- tools
- 28
- transport
- STDIO
- last updated
- Feb 9, 2026
Tools
28 toolsPublic tool metadata for what this MCP can expose to an agent.
search_uniprotSearch UniProt by protein name, gene, or ID
Search UniProt by protein name, gene, or ID
No parameter schema in public metadata yet.
get_protein_detailsGet detailed protein info (function, domains, GO terms)
Get detailed protein info (function, domains, GO terms)
No parameter schema in public metadata yet.
search_ncbi_geneSearch NCBI Gene database
Search NCBI Gene database
No parameter schema in public metadata yet.
search_ensembl_geneGet gene location and details from Ensembl
Get gene location and details from Ensembl
No parameter schema in public metadata yet.
get_variant_infoGet SNP/variant info by rsID
Get SNP/variant info by rsID
No parameter schema in public metadata yet.
get_interpro_domainsGet protein domain information
Get protein domain information
No parameter schema in public metadata yet.
search_clinvarSearch ClinVar for clinical variants
Search ClinVar for clinical variants
No parameter schema in public metadata yet.
get_clinvar_variantGet clinical interpretation for a variant
Get clinical interpretation for a variant
No parameter schema in public metadata yet.
annotate_snpsAnnotate SNPs with functional consequences
Annotate SNPs with functional consequences
No parameter schema in public metadata yet.
query_gwas_catalogQuery GWAS Catalog for associations
Query GWAS Catalog for associations
No parameter schema in public metadata yet.
get_eqtl_dataGet eQTL data from GTEx
Get eQTL data from GTEx
No parameter schema in public metadata yet.
get_protein_interactionsFind interacting proteins (STRING)
Find interacting proteins (STRING)
No parameter schema in public metadata yet.
get_interaction_networkGet network between multiple proteins
Get network between multiple proteins
No parameter schema in public metadata yet.
get_functional_enrichmentPathway/GO enrichment analysis
Pathway/GO enrichment analysis
No parameter schema in public metadata yet.
get_alphafold_structureGet AI-predicted structure
Get AI-predicted structure
No parameter schema in public metadata yet.
search_alphafoldSearch AlphaFold database
Search AlphaFold database
No parameter schema in public metadata yet.
search_pdb_structuresSearch PDB for 3D structures
Search PDB for 3D structures
No parameter schema in public metadata yet.
get_pdb_structureGet PDB structure details
Get PDB structure details
No parameter schema in public metadata yet.
search_kegg_pathwaySearch KEGG pathways
Search KEGG pathways
No parameter schema in public metadata yet.
get_kegg_pathwayGet pathway genes and details
Get pathway genes and details
No parameter schema in public metadata yet.
get_gene_pathwaysFind pathways for a gene
Find pathways for a gene
No parameter schema in public metadata yet.
get_drug_targetsFind drugs targeting a gene (Open Targets)
Find drugs targeting a gene (Open Targets)
No parameter schema in public metadata yet.
get_disease_associationsGet disease associations with scores
Get disease associations with scores
No parameter schema in public metadata yet.
search_open_targetsSearch genes, diseases, or drugs
Search genes, diseases, or drugs
No parameter schema in public metadata yet.
search_pharmgkbSearch PharmGKB database
Search PharmGKB database
No parameter schema in public metadata yet.
get_drug_gene_interactionsGet drug-gene interactions
Get drug-gene interactions
No parameter schema in public metadata yet.
search_omimSearch OMIM for genetic diseases
Search OMIM for genetic diseases
No parameter schema in public metadata yet.
get_gene_diseasesGet all diseases for a gene
Get all diseases for a gene
No parameter schema in public metadata yet.
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🧬 GWAS-MCP: Bioinformatics MCP Server
A powerful Model Context Protocol (MCP) server for GWAS and bioinformatics research. Seamlessly integrates with Claude Desktop and other MCP clients to provide AI-powered access to major biological databases.
✨ Features
🔬 Protein & Gene Lookup
- UniProt - Search proteins by name, gene, or ID
- Ensembl - Gene information and variant details
- NCBI Gene - Comprehensive gene database
Details
- Repository
- github.com/zaeyasa/gwas-mcp
- Package
gwas-mcp- Transport
- STDIO
- Registry
- MCP registry, active