What is the best alternative to Uniprot?

The top-rated alternatives to Uniprot in the Databases category include MCP Toolbox for Databases, Bigquery MCP, Mysql MCP Server. These servers offer complementary or alternative capabilities depending on your deployment stack and authentication requirements.

How do Uniprot alternatives differ in installation and runtime?

Uniprot and its alternatives vary by runtime requirement (Node.js/npx, Python/uvx, Docker, or remote HTTP/SSE endpoints). Check the specification comparison table above to verify command requirements before installing.

Are alternatives to Uniprot free and open source?

Most MCP servers listed on AllMCPs are open source tools under MIT or Apache licenses that you can self-host or run locally with Claude Desktop, Cursor, VS Code, or Windsurf.

How do I side-by-side compare Uniprot with a specific alternative?

Click the "Compare side-by-side →" button on any alternative card to see an in-depth comparison matrix covering feature lists, stars, npm downloads, install configurations, and schema specifications.

Databases• MCP Alternatives Guide

Best Alternatives to Uniprot

Looking for an alternative to Uniprot? Whether you need a different runtime environment, custom authentication support, or alternative API integrations in the Databases ecosystem, we have cataloged and compared the top alternative MCP servers below.

Browse all Databases servers →View Uniprot Specs →

Target Reference Server

Uniprot Overview

UniProt MCP — protein sequence + function database.

Specification Matrix: Uniprot vs Alternatives

Server Name	Runtime	Auth	Pricing	GitHub Stars	Downloads	Action
U Uniprot (Target)	npx	Free/None	Free	—	—	Current
MCP Toolbox for Databases	npx	Free/None	Free	16,329	—	Compare →
Bigquery MCP	uvx	Free/None	Free	10	—	Compare →
Mysql MCP Server	uvx	Other	Free	1,381	—	Compare →
Genai Toolbox	npx	Other	Free	16,315	—	Compare →
Supabase	Remote (SSE)	Free/None	Free	2,889	—	Compare →
Open Food Facts	Remote (SSE)	Free/None	Free	3	—	Compare →
MCP Server Mysql	npx	Other	Free	2,104	—	Compare →
Dagpipe	uvx	Free/None	Free	3	—	Compare →
Wgong Sqlite MCP Server	uvx	Free/None	Free	1	—	Compare →
Legion MCP	npx	Other	Free	94	—	Compare →
Dbhub	npx	Free/None	Free	3,469	—	Compare →
L Legislation Uk	npx	Free/None	Free	—	—	Compare →