"Local" matching MCP servers:

MCP server that provides tools for querying the Human Phenotype Ontology (HPO) including term lookup, hierarchy exploration, cross-ontology mappings, and gene-phenotype-disease associations, all grounded in a local SQLite database for fast offline lookups.

Provides local DNA/RNA sequence analysis tools (composition, reverse complement, translation, ORF enumeration, motif scanning) via MCP for agent workflows.

Integrates AlphaFold DB and eight other biomedical data sources into MCP tools for variant clinical reporting, disease-target analysis, structural intelligence, and drug repurposing, with results persisted to a local SQLite knowledge graph.

Enables AI-driven pharmacogenomic analysis by querying structured genetic variant, drug response, and disease risk data. Supports natural language questions about medications, traits, and health risks based on user genome data, with privacy-first local execution.

Enables users to generate volcano plots by submitting jobs with input files and parameters, supporting local or Docker execution.

Enables AI coding agents to search academic papers, resolve biomedical entities, mine relations, and traverse citation graphs using Semantic Scholar and PubTator3, with local caching for reproducibility.

An MCP server for High-Throughput Screening (HTS) assay calculations across sub-cellular, cellular, tissue, and organism biological tiers, enabling local-first bioassay analysis.

Enables compiling typed decision queries into the smallest decision-sufficient evidence context with machine-checkable Context Certificates, providing auditable executable-biology inference through local MCP tools.

An MCP server that enables AI assistants to generate, score, and analyze DNA sequences using the evo2 genomic foundation model. It supports multiple execution modes including local GPU, SLURM clusters, and the Nvidia NIM cloud API for tasks like variant effect prediction and sequence embedding.

An MCP server for running local LLMs using llama-cpp-python, with built-in tools for generating drug-like molecule SMILES.

An MCP server providing public plant bioinformatics APIs including UniProt, NCBI, InterProScan, PDB, AlphaFold, Ensembl Plants, and web-based resources like Sol Genomics and BAR, without local data. It supports gene lookups, protein summaries, structure retrieval, and functional annotations through natural language.

Enables installing, configuring, and running modular MCP servers for biology, bioinformatics, and bioimaging tasks, including local image analysis, ImageJ/Fiji bridging, and LLM-based agent workflows.

A local-first MCP server that annotates whole-genome VCF files and lets you query pharmacogenomics, disease risk, and carrier status through natural language.

Wraps NCBI BLAST+ blastp into a FastMCP service for auditable protein homology searches with local output artifacts and structured metadata.

Provides protein family, domain, and functional annotation using InterProScan, supporting local or API backends.

Manages local protein experiments with a Flask backend and SQLite, offering tools for protein library management, Beer-Lambert concentration calculations, BLI dilution planning, and experiment archiving. It provides 7 MCP tools for AI assistants like Claude to interact with the system.