ensembl-sequence-retrieval

---
name: ensembl-sequence-retrieval
description: Retrieve genomic sequences from Ensembl database using transcript or gene IDs to obtain nucleotide and protein sequences.
license: MIT license
metadata:
    skill-author: PJLab
---

# Ensembl Sequence Retrieval

## Usage

### 1. MCP Server Definition

```python
import asyncio
import json
from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession

class OrigeneClient:
    """Origene-Ensembl MCP Client"""

    def __init__(self, server_url: str, api_key: str):
        self.server_url = server_url
        self.api_key = api_key
        self.session = None

    async def connect(self):
        try:
            self.transport = streamablehttp_client(
                url=self.server_url,
                headers={"SCP-HUB-API-KEY": self.api_key}
            )
            self.read, self.write, self.get_session_id = await self.transport.__aenter__()
            self.session_ctx = ClientSession(self.read, self.write)
            self.session = await self.session_ctx.__aenter__()
            await self.session.initialize()
            return True
        except Exception as e:
            print(f"✗ connect failure: {e}")
            return False

    async def disconnect(self):
        try:
            if self.session:
                await self.session_ctx.__aexit__(None, None, None)
            if hasattr(self, 'transport'):
                await self.transport.__aexit__(None, None, None)
        except Exception as e:
            print(f"✗ disconnect error: {e}")

    def parse_result(self, result):
        if isinstance(result, dict):
            content_list = result.get("content") or []
        else:
            content_list = getattr(result, "content", []) or []
        texts = []
        for item in content_list:
            if isinstance(item, dict):
                if item.get("type") == "text":
                    texts.append(item.get("text") or "")
            else:
                if getattr(item, "type", None) == "text":
                    texts.append(getattr(item, "text", "") or "")
        return "".join(texts)
```

### 2. Sequence Retrieval Workflow

**Implementation:**

```python
## Initialize client
client = OrigeneClient(
    "https://scp.intern-ai.org.cn/api/v1/mcp/12/Origene-Ensembl",
    "<your-api-key>"
)

if not await client.connect():
    print("connection failed")
    exit()

## Retrieve sequence by Ensembl ID
result = await client.session.call_tool(
    "get_sequence_id",
    arguments={
        "id": "ENST00000380152"
    }
)

result_data = client.parse_result(result)
print(result_data)

await client.disconnect()
```

### Tool Descriptions

**Origene-Ensembl Server:**
- `get_sequence_id`: Retrieve sequence by Ensembl ID
  - Args:
    - `id` (str): Ensembl transcript or gene ID
  - Returns: Genomic or protein sequence

### Use Cases

- Genome annotation
- Comparative genomics
- Transcript analysis
- Protein sequence retrieval