Mysql MCP Server vs Uniprot
A side-by-side look at the Mysql MCP Server and Uniprot MCP servers: transport, auth, tools, quality signals, and the config to install either one in Claude, Cursor, Windsurf or VS Code.
Verdict: choose Mysql MCP Server for databases work as a local process; choose Uniprot for databases as a local process. You can also run both side by side in one mcpServers block.
Which MCP server should you choose?
Choose Mysql MCP Server when
- You need dedicated capabilities in the Databases domain.
- You prefer a local stdio subprocess transport.
- Its auth model fits you: other.
- You have the keys it needs:
MYSQL_HOST, MYSQL_USER, MYSQL_PASSWORD. - You want tools like
execute_sql, get_schema_info, get_table_sample.
Choose Uniprot when
- You need dedicated capabilities in the Databases domain.
- You prefer a local stdio subprocess transport.
- You want tools like
search, get, proteomes_search.
Feature & specification comparison
Rows where the two servers differ are marked.
| Spec | ||
|---|---|---|
| Category | Databases | Databases |
| Quality signal | 56/100 · Good | 57/100 · Good |
| Install command | Confirmed | Confirmed |
| Transport | Local subprocess (stdio) | Local subprocess (stdio) |
| Auth | other | Not declared |
| Pricing | Free | Not declared |
| Required env vars | MYSQL_HOSTMYSQL_USERMYSQL_PASSWORD | None listed |
| Verified owner | Community listing | Community listing |
| GitHub stars | 1,400 | 0 |
| Directory activity | 4 views 0 installs 1 upvotes | 1 views 0 installs 0 upvotes |
| Tools | 3 | 6 |
| Full listing | View Mysql MCP Server | View Uniprot |
Tools & capabilities
Mysql MCP Server tools 3
execute_sqlExecutes any standard SQL query.get_schema_infoProvides detailed metadata about database structures.get_table_sampleFetches a representative sample of data.
Uniprot tools 6
search"Find protein [name]" / "look up [gene] in UniProt" / "BRCA1 / TP53 / insulin protein info" / "all proteins for [organism]" — UniProtKB search via Lucene-style queries (e.g. gene:BRCA1 AND organism_id:9606 for human BRCA1). UniProt is the authoritative protein-sequence-and-function database — use for protein characterization, function annotation, sequence retrieval, and cross-references to PDB/GO/PubMed.get"Fetch protein [P12345]" / "UniProt entry for [accession]" / "FASTA sequence for [protein]" — single UniProtKB entry by accession (e.g. P12345 or P38398 for BRCA1_HUMAN). Returns full protein record: sequence, function annotations, GO terms, cross-refs, post-translational modifications, variants. Pass format=fasta for sequence only.proteomes_search"Reference proteome for [organism]" / "complete protein set of [species]" — search UniProt reference proteomes (the curated representative protein set per organism). Use as a starting point for genome-scale protein analyses.taxonomy_search"NCBI taxonomy ID for [organism]" / "taxid for [species]" / "look up [Latin name] in NCBI taxonomy" — search NCBI Taxonomy via UniProt's mirror. Returns taxonomic IDs you can use as organism_id filters in `search` (9606 = human, 10090 = mouse, 7227 = D. melanogaster, etc).keyword"UniProt keyword KW-N info" / "what does keyword [X] mean" — fetch a UniProt controlled-vocabulary keyword by ID. Use to look up annotation tags like "Kinase" / "Membrane" / "Disease-associated".feature_summary"Domain map of [protein]" / "annotated features of [accession]" / "what regions / sites does [protein] have" — annotated features (domains, active sites, transmembrane regions, mutagenesis sites, glycosylation, disulfide bonds, etc.) for a UniProt accession. Use for structural/functional analysis without pulling the full protein record.
Ready-to-paste client configs
Paste either block (or both) into your client config, e.g. claude_desktop_config.json or ~/.cursor/mcp.json. We only show a config when the install command is confirmed.
Mysql MCP Server
{
"mcpServers": {
"designcomputer-mysql-mcp-server": {
"command": "uvx",
"args": [
"mysql_mcp_server"
],
"env": {
"MYSQL_HOST": "YOUR_MYSQL_HOST_HERE",
"MYSQL_USER": "YOUR_MYSQL_USER_HERE",
"MYSQL_PASSWORD": "YOUR_MYSQL_PASSWORD_HERE"
}
}
}
}
Uniprot
{
"mcpServers": {
"uniprot": {
"command": "npx",
"args": [
"-y",
"@pipeworx/mcp-uniprot"
]
}
}
}
Frequently asked questions
Mysql MCP Server is categorized under Databases and uses a local stdio subprocess. Uniprot belongs to Databases and uses a local stdio subprocess. Pick Mysql MCP Server for databases work and Uniprot for databases.
Copy the mcpServers block from the config section on this page into your client's config (for example claude_desktop_config.json or ~/.cursor/mcp.json), then fully restart the client.
Mysql MCP Server is listed as free. Auth: other. Uniprot has no declared pricing — check the project's own site. If a server needs environment variables such as API keys, define them under the env key in your client's MCP config.
Yes. MCP clients support multiple servers: add designcomputer-mysql-mcp-server and uniprot as separate keys in the same mcpServers object, and your assistant will call tools from either one.
On AllMCPs, Mysql MCP Server has a quality signal of 56/100 (Good) with 4 views, 0 installs and 1,400 GitHub stars. Uniprot has 57/100 (Good) with 1 views, 0 installs and 0 GitHub stars.