uniprot-protein-retrieval

name	uniprot-protein-retrieval
description	Retrieve protein sequences and functional information from UniProt database by protein name, enabling protein analysis and bioinformatics workflows.
license	MIT license
metadata	{"skill-author":"PJLab"}

UniProt Protein Sequence Retrieval

Usage

1. MCP Server Definition

Use the standard MCP client pattern for Origene-UniProt server.

2. Protein Sequence Retrieval Workflow

This workflow retrieves protein sequences and associated information from the UniProt database using protein names or identifiers.

Workflow Steps:

1. Query by Protein Name - Search UniProt using common protein names
2. Retrieve Sequence Data - Get amino acid sequence and metadata

Implementation:

from mcp.client.streamable_http import streamablehttp_client
from mcp import ClientSession
import json
from contextlib import AsyncExitStack

class OrigeneClient:
    def ():
        .server_url = server_url
        .session = 

      ():
        :
            .transport = streamablehttp_client(
                url=.server_url,
                headers={: }
            )
            ._stack = AsyncExitStack()
             ._stack.__aenter__()
            .read, .write, .get_session_id =  ._stack.enter_async_context(.transport)
            .session_ctx = ClientSession(.read, .write)
            .session =  ._stack.enter_async_context(.session_ctx)
             .session.initialize()
            ()
             
         Exception  e:
            ()
             

      ():
        
        :
             (, ):
                 ._stack.aclose()
            ()
         Exception  e:
            ()
     ():
        :
             (result, )  result.content:
                content = result.content[]
                 (content, ):
                     json.loads(content.text)
             (result)
         Exception  e:
             {: , : (result)}


client = OrigeneClient()
   client.connect():
    ()
    


protein_name =   

result =  client.session.call_tool(
    ,
    arguments={
        : protein_name
    }
)

result_data = client.parse_result(result)


()
( * )

   result_data:
    sequence = result_data[]
    ()
    (sequence)

    
    ()
     i  (, (sequence), ):
        position = i + 
        block = sequence[i:i+]
        ()

   result_data:
    ()

   result_data:
    ()

   result_data:
    ()

   result_data:
    ()

 client.disconnect()