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Unofficial Ensembl MCP Server

@Augmented-Nature

代码仓库

基本信息

分类

其他

许可证

MIT license

传输方式

stdio

作者

Augmented-Nature

关于 Unofficial Ensembl MCP Server

A comprehensive Model Context Protocol (MCP) server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations.

#ensembl#genomics#bioinformatics

Unofficial Ensembl MCP Server 配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

{
  "mcpServers": {
    "ensembl": {
      "command": "node",
      "args": [
        "/path/to/ensembl-server/build/index.js"
      ]
    }
  }
}

Unofficial Ensembl MCP Server 工具

工具列表暂未提供

当前收录暂时没有可展示的工具列表，不代表服务没有工具。请查阅项目文档了解支持的能力。

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

What is Unofficial Ensembl MCP Server?

An MCP server that provides access to the Ensembl REST API for genomic data, comparative genomics, and biological annotations. Developed by Augmented Nature, it enables gene lookups, sequence retrieval, variant analysis, regulatory features, and more across multiple species through a standardized interface.

How to use Unofficial Ensembl MCP Server?

Install dependencies with npm install, build with npm run build, then configure in Claude Desktop as an MCP server using the command node with arguments pointing to the built index.js. After setup, use natural language queries like "Look up the BRCA2 gene" to access genomic data.

Key features of Unofficial Ensembl MCP Server

  • Gene lookup by Ensembl ID or symbol
  • DNA, CDS, and protein sequence retrieval
  • Variant retrieval and consequence prediction
  • Ortholog and paralog detection across species
  • Access to regulatory elements and motif features
  • Batch processing for multiple genes or regions

Use cases of Unofficial Ensembl MCP Server

  • Look up a gene and retrieve its genomic sequence
  • Find orthologs of a human gene in mouse
  • Get all genetic variants within a specific genomic region
  • Search for genes related to a biological function (e.g., insulin)
  • Obtain assembly information and karyotype for a species

常见问题

1

What species are supported?

All species available in Ensembl are supported, including vertebrates, plants, fungi, protists, and metazoa. The default species is `homo_sapiens`.

2

What input formats are accepted?

Genomic regions (e.g., `chr1:1000000-2000000`), Ensembl IDs (e.g., `ENSG00000139618`), gene symbols (e.g., `BRCA2`), and RefSeq IDs (e.g., `NM_000059`) are all valid inputs.

3

What are the rate limits?

The server respects Ensembl's guidelines: maximum 15 requests per second, with appropriate delays between batch operations and connection pooling for efficiency.

4

What output formats are available?

Primary formats include JSON, FASTA, GFF, and VCF. Phylogenetic trees support JSON, Newick, and PhyloXML formats.

5

How can I configure the server?

Set environment variables `ENSEMBL_BASE_URL` to override the default API base URL and `REQUEST_TIMEOUT` to change the timeout (default 30000ms). The default species is configurable.

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