Provides tools to retrieve PubMed reference details—title, journal, authors, and DOI—for PubMed IDs associated with AMR gene records.
This server does not currently have a deployable release on Glama. Follow the repository's setup instructions to install and configure it for your MCP client, including any required credentials and local dependencies.
An MCP server that lets AI assistants (Claude, Codex, Cursor…) query antimicrobial resistance (AMR) data from public, free sources:
NCBI Reference Gene Catalog, the curated database behind AMRFinderPlus: ~11,500 AMR genes, point mutations, stress and virulence genes
NCBI E-utilities: protein and nucleotide sequences, PubMed references
UniProtKB: protein function, keywords and cross-references
AMRFinderPlus (optional, if installed locally): screen your own genomes
All data sources are public domain or freely accessible; no API keys are required.
Which carbapenemases are reported in Klebsiella pneumoniae, and what is the original paper for KPC-2?
Give me the protein sequence of mcr-1.1 and its UniProt function annotation.
Run AMRFinderPlus on
~/data/isolate_17.fastaas Escherichia and explain the hits by drug class.
Related MCP server: veupathdb-wdk-mcp
Tool | What it does |
| Search by text, drug class, subclass, organism or element type |
| Exact record for an allele ( |
| Drug classes and how many catalog entries each has |
| Catalog version and size |
| Protein or nucleotide FASTA from NCBI by accession |
| Title, journal, authors and DOI for PubMed IDs |
| UniProtKB search and entry details |
| Run a local AMRFinderPlus install on a FASTA file |
Run it with uv (no install step needed), or pip install amr-mcp.
claude mcp add amr -- uvx amr-mcpAdd to claude_desktop_config.json:
{
"mcpServers": {
"amr": { "command": "uvx", "args": ["amr-mcp"] }
}
}pipx install amr-mcp
which amr-mcp # e.g. /Users/you/.local/bin/amr-mcpThen use that absolute path as the command, for example in claude_desktop_config.json:
{
"mcpServers": {
"amr": { "command": "/Users/you/.local/bin/amr-mcp" }
}
}Desktop apps don't inherit your shell's PATH, so if Claude Desktop can't start the server,
use the absolute path for the command (this applies to uvx too: run which uvx to get it).
Variable | Purpose |
| Optional, free. Raises the NCBI rate limit from 3 to 10 requests/s |
| Optional. Contact e-mail NCBI asks tools to send |
| Where the catalog is cached (default |
To enable run_amrfinder: conda install -c bioconda ncbi-amrfinderplus && amrfinder -u.
python -m venv .venv && .venv/bin/pip install -e ".[dev]"
.venv/bin/pytest -m "not network" # offline tests
.venv/bin/pytest # also hits the live NCBI/UniProt APIsThe NCBI Reference Gene Catalog and NCBI sequence data are US government works in the public domain. UniProt data is available under CC BY 4.0. Please cite the original sources when you publish results:
Feldgarden M, et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep. 2021.
The UniProt Consortium. UniProt: the Universal Protein Knowledgebase. Nucleic Acids Res.
MIT
Developed with AI assistance (Claude Code); all code reviewed and tested by the author.
This server cannot be deployed
Pharmacogenomics for AI agents: cited drug–gene, gene and rsID lookups plus a medication screen.
Connect AI clients to biomedical data and tools.
Find pharmacogenomics guidelines, translate diplotypes, and retrieve prescribing recommendations.
Search biomedical literature, get article details, find related articles, and explore MeSH terms
