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  • Biomart MCP

    jzinno
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    A Model Context Protocol server that interfaces with Biomart databases, allowing models to discover biological datasets, explore attributes/filters, retrieve biological data, and translate between different biological identifiers.
    Last updated
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    MIT

  • Rosetta MCP Server

    Arielbs
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    An MCP server that enables AI coding assistants to interact with Rosetta, PyRosetta, and Biotite for running RosettaScripts, validating XML, translating between Rosetta and Biotite, scoring structures, and querying documentation.
    Last updated
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    16
    MIT

  • miEAA3 MCP Server

    kkShrihari
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    Integrates the miEAA 3.x bioinformatics platform with Claude Desktop, enabling microRNA enrichment analysis, identifier conversion between miRBase versions, and miRNA-precursor transformations through natural language.
    Last updated
    4
  • Bio-MCP FastQC Server by bio-mcp

    Bio-MCP FastQC Serverofficial

    bio-mcp
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    Enables AI assistants to perform quality control analysis on high-throughput sequencing data using FastQC and MultiQC. It supports single-file and batch processing of FASTQ/FASTA files and generates comprehensive, interactive summary reports.
    Last updated
    MIT
  • bio-mcp-evo2 by bio-mcp

    bio-mcp-evo2official

    bio-mcp
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    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.
    Last updated
    MIT
  • galaxy-mcp by galaxyproject

    galaxy-mcpofficial

    galaxyproject
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    MCP server for interacting with Galaxy bioinformatics platform, enabling AI assistants to connect to Galaxy instances, search and execute tools, manage workflows, and access other features.
    Last updated
    36
    MIT

  • BWA MCP Server

    bio-mcp
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    Enables AI assistants to perform DNA/RNA sequence alignment using BWA (Burrows-Wheeler Aligner), supporting both short and long read alignment to reference genomes with indexing, BWA-MEM, and BWA-backtrack algorithms.
    Last updated
    MIT

  • Oh My KEGG MCP

    martinuslee
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    An MCP server that provides access to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, offering 30 tools for searching and analyzing biological data like pathways, genes, and compounds. It supports integration with LangChain and Ollama to enable LLMs to interact with comprehensive genomic and chemical datasets.
    Last updated
    8
    MIT

  • methods-mcp

    webwebb56
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    Provides MCP tool adapters for Bioconductor methods like limma, DESeq2, and fgsea, enabling statistical analysis of omics data through containerized R execution. It serves as a bridge between MCP clients and bioinformatics tools for reproducible research workflows.
    Last updated
    Apache 2.0

  • refua-mcp

    agentcures
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    MCP server for biological protein design, folding, and affinity prediction using Refua tools, with optional support for ADMET, clinical simulation, preclinical planning, wet-lab automation, and more.
    Last updated
    MIT

  • Aurora-MCP

    ndaniel
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    Enables querying relationships between plant species, small molecules, and mitochondrial Complex I inhibitors by bridging natural-product, biodiversity, and PubMed datasets. Allows LLMs to perform structured searches and reasoning over biological data to identify potential plant-derived mitochondrial inhibitors.
    Last updated
    GPL 3.0

  • ChemDraw Server

    tom832
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    Provides chemical informatics endpoints for converting between chemical names and SMILES, processing molecule structures, and comparing molecules, with MCP compatibility.
    Last updated
    4
    MIT

  • bioRxiv-MCP-Server

    JackKuo666
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    🔍 Enable AI assistants to search and access bioRxiv papers through a simple MCP interface. The bioRxiv MCP Server provides a bridge between AI assistants and bioRxiv's preprint repository through the Model Context Protocol (MCP). It allows AI models to search for biology preprints and access their
    Last updated
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