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Liftover MCP server

@koido

リポジトリ

基本情報

カテゴリ

その他

ライセンス

Apache-2.0

トランスポート

stdio

作者

koido

投稿者

Masaru Koido

Liftover MCP server について

概要はまだありません

#liftover#bioinformatics#genetics

Liftover MCP server の設定

以下の設定を使って、このサーバーを MCP 対応クライアントに追加してください。

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

Liftover MCP server のツール

ツール一覧はまだありません

この掲載には表示できるツール一覧がまだありません。サーバーにツールがないという意味ではありません。対応機能はプロジェクトのドキュメントをご確認ください。

ツールは README から自動的に抽出されます。メンテナーは ## Tools という見出しの下に記載することで、このタブに反映できます。

概要

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

よくある質問

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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