Enable AI assistants to perform BLAST searches through natural language. Search nucleotide and protein databases, create custom databases, and get
Connect Bio MCP Blast to Claude, Cursor or any other MCP client and it stops being a tab you switch to. Enable AI assistants to perform BLAST searches through natural language. Search nucleotide and protein databases, create custom databases, and get formatted results instantly. The bio mcp blast mcp server is what makes that connection.
The toolset is worth reading before you wire it up, because it tells you what the integration is really for:
Installation — The Installation tool exposed by this serverConfiguration — The Configuration tool exposed by this serverblastn — The blastn tool exposed by this serverblastp — The blastp tool exposed by this servermakeblastdb — The makeblastdb tool exposed by this serverSetup — The Setup tool exposed by this serverUsage — The Usage tool exposed by this serverSandboxing — The Sandboxing tool exposed by this serverSetup follows the usual MCP pattern — install or clone the server, register it in your client's configuration file, restart the client. The configuration blocks on this page cover the common clients.
Configuration is passed through the environment: BIO_MCP_MAX_FILE_SIZE, BIO_MCP_TIMEOUT, BIO_MCP_BLAST_PATH, BIO_MCP_QUEUE_URL, BLASTDB, BLAST_NUM_THREADS. Treat anything key-shaped as a real credential — scope it to the minimum the server needs, and rotate it if it ever lands in a shared config.
Among the developer tooling options, the useful question is rarely "what can it do" but "what does it cost you to run" — permissions, credentials, and how much of your context its toolset consumes. Bio MCP Blast's toolset — Installation, Configuration, blastn and 5 more — is a fair guide to whether it matches your workflow. It is maintained by bio-mcp; worth a glance at recent repository activity before you build anything load-bearing on it.
SyncDev reviews every entry in this directory against the project's own documentation before publishing, and revisits them as servers change.
| Tool | What it does |
|---|---|
| Installation | The Installation tool exposed by this server. |
| Configuration | The Configuration tool exposed by this server. |
| blastn | The blastn tool exposed by this server. |
| blastp | The blastp tool exposed by this server. |
| makeblastdb | The makeblastdb tool exposed by this server. |
| Setup | The Setup tool exposed by this server. |
| Usage | The Usage tool exposed by this server. |
| Sandboxing | The Sandboxing tool exposed by this server. |
{
"mcpServers": {
"bio-blast": {
"command": "python",
"args": ["-m", "src.server"],
"cwd": "/path/to/bio-mcp-blast"
}
}
}Configuration as documented by the project. Restart the client after saving.
| Variable | Description | Required |
|---|---|---|
| BIO_MCP_MAX_FILE_SIZE | Configuration value read at startup. | Optional |
| BIO_MCP_TIMEOUT | Configuration value read at startup. | Optional |
| BIO_MCP_BLAST_PATH | Filesystem location the server is allowed to use. | Optional |
| BIO_MCP_QUEUE_URL | Endpoint or connection string the server talks to. | Yes |
| BLASTDB | Configuration value read at startup. | Optional |
| BLAST_NUM_THREADS | Configuration value read at startup. | Optional |
The simplest web tool that matters — fetch any URL and get model-ready markdown back.
Industrial-strength web extraction — render, scrape, crawl and search entire sites into clean markdown.
Puppeteer-powered browser control that drives pages from the accessibility tree instead of pixels.
Search built for AI, not humans — semantic web search that returns model-ready content, plus code context.
Answers, not links — delegate questions to Perplexity's search-grounded models and get cited responses back.
Put 6,000+ pre-built scrapers at your assistant's fingertips through one MCP endpoint.