BLAST (Bio-MCP)

MCP server that lets Claude run NCBI BLAST+ sequence-similarity searches against local or custom databases.


Type	MCP server (stdio; optional HTTP job queue)
Supplier	Bio-MCP (community OSS)
Availability	GA — public GitHub repo, MIT-licensed
Pricing	Free / OSS (MIT)
Capabilities	Read/Write — runs BLAST+ binaries locally; can build databases (`makeblastdb`)
Verified	works · 2026-07-20
Security	caution · 2026-07-20 — no LICENSE file upstream despite MIT claim, unmaintained since 2025-06, no OSV advisories

How to install

BLAST+ binaries must be on your PATH first, then clone and install the server.

Install the BLAST+ binaries (prerequisite — the server shells out to them):
```
conda install -c bioconda blast
```
(macOS alternative: brew install blast; Ubuntu: sudo apt install ncbi-blast+.)

Clone and install the server:

git clone https://github.com/bio-mcp/bio-mcp-blast.git
cd bio-mcp-blast
pip install -e .

(Optional) verify it starts, then Ctrl-C — Claude launches the process itself via stdio, so you do not keep this running:
```
python -m src.server
```
Register it.
- Claude Code (stdio) — run from inside the cloned bio-mcp-blast directory so $(pwd) resolves, or substitute the absolute clone path:
```
claude mcp add --transport stdio bio-blast -- python -m src.server
```
  (run this with the working directory set to your clone, e.g. cd /path/to/bio-mcp-blast first — replace /path/to/bio-mcp-blast with the absolute path of your clone, or $(pwd) if you are still inside it from the previous step)
- Claude Desktop — add to claude_desktop_config.json (cwd must be the absolute path of your clone):
```
{
  "mcpServers": {
    "bio-blast": {
      "command": "python",
      "args": ["-m", "src.server"],
      "cwd": "/path/to/bio-mcp-blast"
    }
  }
}
```
  (replace /path/to/bio-mcp-blast with the absolute path of your clone — e.g. /Users/you/repos/bio-mcp-blast)

What it does

Exposes BLAST+ as MCP tools:

blastn — nucleotide-vs-nucleotide search
blastp — protein-vs-protein search
makeblastdb — build a custom BLAST database from a FASTA file
blastn_async / blastp_async — queue-based async variants for long searches
get_job_status / get_job_result — monitor and retrieve async-job output

Primary use cases: Sequence-similarity search for gene/protein identification, screening contigs and amplicons against custom databases, microbial/metagenomic homology lookups.

Notes

Primary transport is stdio (python -m src.server); Claude Code/Desktop launch the process. The async tools optionally use a separate HTTP job queue (bio-mcp-queue, --queue-url http://localhost:8000) for long-running searches — that queue is a long-lived service you must start separately and is not required for the synchronous blastn/blastp tools. Part of the broader Bio-MCP collection (samtools, bcftools, seqkit, bwa, bedtools, fastqc, interpro, evo2), each a discrete per-tool MCP server sharing this clone-and-pip install -e . pattern. Tagged All because sequence-similarity search is a cross-cutting primitive across every life-science domain.

Sources

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