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20 Best MySQL MCP Servers: compared and ranked, October 2026Ranked from 574 matching servers on stars, growth, downloads and maintenance. Updated .

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  • A
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    A Model Context Protocol server providing LLMs with access to the Ensembl genomics database, enabling AI assistants to query gene information, sequences, variants, and other genomic data across multiple species.
    10
    8
    JavaScript
    MIT
  • F
    license
    A
    quality
    F
    maintenance
    A Model Context Protocol (MCP) server that provides access to the Protein Data Bank (PDB) - the worldwide repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies.
    5
    26
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    B
    quality
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    Provides a programmatic interface to the Genome Aggregation Database (gnomAD) API across versions v2.1.1, v3.1.2, and v4.1.0. It enables users to query gene metadata, variant information, population frequencies, and ClinVar data through a unified schema.
    12
    6
    Apache 2.0
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    B
    quality
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    Provides seamless access to UniProtKB protein database, enabling queries for protein entries, sequences, Gene Ontology annotations, full-text search, and ID mapping across 200+ database types.
    5
    16 PyPI
    2
    MIT
  • A
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    B
    quality
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    Enables comprehensive access to PubChem's chemical database with over 110 million compounds. Supports chemical searches, structure analysis, bioactivity data, safety information, and molecular property calculations through 30 specialized tools.
    30
    MIT
  • F
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    B
    quality
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    Enables AI assistants to query genetic variant data, gene constraints, and population genetics information from the gnomAD (Genome Aggregation Database) through its GraphQL API. Supports searching for genes and variants, retrieving constraint scores, analyzing population frequencies, and accessing genomic coverage data.
    9
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  • A
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    Enables AI agents to search and retrieve compounds, drugs, diseases, pathways, genes, enzymes, glycans, modules, and KO entries; fetch full parsed flat-file entries by ID; and list database contents through keyless REST tools.
    362 npm
    MIT
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    C
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    MCP server that exposes STRING database functionality, allowing AI agents to resolve protein identifiers, retrieve interaction networks, perform homology lookups, and run functional enrichment analysis.
    7
    MIT
  • A
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    quality
    B
    maintenance
    Enables AI agents to resolve marine species names to OBIS taxon records, retrieve georeferenced ocean occurrence records with optional date filtering, and pull aggregate statistics such as record counts, contributing datasets, and observed year ranges. Queries the Ocean Biodiversity Information System keylessly over the Pipeworx gateway or as a local stdio server.
    358 npm
    MIT
  • A
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    quality
    C
    maintenance
    Enables querying NCBI genome assemblies, gene details with cross-references, and taxonomy trees with per-node assembly and gene counts, providing structured answers about genomes, genes, and taxonomy.
    247 npm
    MIT
  • A
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    Not graded
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    B
    maintenance
    Enables users to look up yeast genes/loci, search genes and alleles by free text, and retrieve Gene Ontology annotations from the Saccharomyces Genome Database.
    307 npm
    MIT
  • A
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    A
    maintenance
    Enables looking up genes, fetching sequences, predicting variant consequences, finding orthologs, and cross-database xrefs via Ensembl REST API through MCP.
    431 npm
    3
    Apache 2.0
  • A
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    Not graded
    quality
    B
    maintenance
    Enables querying metadata from MyVariant.info, a comprehensive variant annotation database, providing dataset statistics, source information, and build versions.
    1 npm
    MIT
  • A
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    Not graded
    quality
    C
    maintenance
    Enables querying the BOLD Systems global DNA barcode database for specimen records, taxonomy, barcode sequences, and BIN clusters, with keyless access and FASTA-ready output.
    MIT