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Liftover MCP server

@koido

代码仓库

基本信息

分类

其他

许可证

Apache-2.0

传输方式

stdio

作者

koido

提交者

Masaru Koido

关于 Liftover MCP server

暂无概览

#liftover#bioinformatics#genetics

Liftover 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": {
    "liftover-mcp": {
      "command": "uv",
      "args": [
        "sync"
      ]
    }
  }
}

Liftover 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 Liftover MCP server?

It provides a programmatic interface to the Broad Institute's Liftover tool, enabling genomic coordinate conversion between different genome assemblies (e.g., hg19 to hg38) via the Model Context Protocol. It is intended for developers and bioinformaticians who need to automate liftover operations.

How to use Liftover MCP server?

Install dependencies with uv sync, then run uv run server.py or add the server to your MCP client configuration (e.g., in Cursor) using uv as the command. Invoke the liftover tool with the required from_genome and to_genome parameters plus one of the supported input formats (single position, interval, variant, or HGVS notation).

Key features of Liftover MCP server

  • Single position conversion between genome builds
  • Interval conversion (start/end coordinates)
  • Variant conversion (chr/pos/ref/alt)
  • HGVS notation conversion (transcript, c., p.)
  • Direct integration with Broad Institute's Liftover web service

Use cases of Liftover MCP server

  • Convert a single genomic coordinate from hg19 to hg38
  • Map a genomic interval (e.g., 141310715–141310720) to a different assembly
  • Transform a variant call (chr, position, ref, alt) between genome builds
  • Convert HGVS notation (e.g., c.875A>T) from one reference genome to another

常见问题

1

What dependencies does Liftover MCP server require?

It requires `uv`, `mcp[cli]`, `fastmcp`, `beautifulsoup4`, and `selenium`.

2

Is Liftover MCP server stable?

It is under active development (alpha release v0.1.0-alpha). Features and APIs may change without notice.

3

Where does the coordinate conversion happen?

All coordinate conversion functionality is provided by the Broad Institute's Liftover web service at liftover.broadinstitute.org.

4

How do I cite or credit this tool?

Credit the Broad Institute's Liftover service when using this tool in your work. The server itself is licensed under Apache License 2.0.

5

What input formats are supported?

Single position (chr + position), interval (chr + start + end), variant (chr + position + ref + alt), and HGVS notation (transcript + c_dot + p_dot). The `from_genome` and `to_genome` parameters are always required.

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