Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add thesecondfox/skill --skill bio-database-access-local-blastgit clone --depth 1 https://github.com/thesecondfox/skillWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-local-blast)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-local-blast"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-local-blast/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-database-access-local-blast"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-database-access-local-blast.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00045 | $0.03093 |
| Opus 5.5 | $0.00018 | $0.01237 |
| Sonnet 5.5 | $0.00009 | $0.00619 |
| Haiku 4.5 | $0.00005 | $0.00309 |
Grade B, and why
bio-local-blast scanned grade B with 2 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 1mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Asks for rootmediumPrivilege escalation
A mod that escalates privileges can change anything on the machine, not only the project.
sudo apt install ncbi-blast+ Runs shell commandslowCapability
Expected in a hook, worth knowing in a rule or an instructions file.
subprocess.run(cmd, check=True) How it starts
The opening of the file, as written. The whole thing — 354 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: NCBI BLAST+ 2.15+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto confirm flags
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Local BLAST
"Run a BLAST search against my custom database" → Build a local BLAST database and search it with query sequences, returning tabular results with identity and e-value.
- CLI:
makeblastdb,blastn/blastp(NCBI BLAST+) - Python:
subprocesswrapper for BLAST+
Run BLAST searches locally using NCBI BLAST+ command-line tools.
Installation (NCBI BLAST+)
# macOS
brew install blast
# Ubuntu/Debian
sudo apt install ncbi-blast+
# conda
conda install -c bioconda blast
# Verify installation
blastn -version
BLAST+ Programs
| Command | Query | Database | Description |
|---|---|---|---|
blastn |
DNA | DNA | Nucleotide-nucleotide |
blastp |
Protein | Protein | Protein-protein |
blastx |
DNA | Protein | Translated query vs protein |
tblastn |
Protein | DNA | Protein vs translated DB |
tblastx |
DNA | DNA | Translated vs translated |
makeblastdb |
- | - | Create BLAST database |
Creating BLAST Databases
makeblastdb - Create Database (NCBI BLAST+)
# Create nucleotide database
makeblastdb -in sequences.fasta -dbtype nucl -out my_db
# Create protein database
makeblastdb -in proteins.fasta -dbtype prot -out my_proteins
# With title and parse sequence IDs
makeblastdb -in sequences.fasta -dbtype nucl -out my_db \
-title "My Reference Database" -parse_seqids
Key Options:
| Option | Description | Values |
|---|---|---|
-in |
Input FASTA file | Path |
-dbtype |
Database type | nucl, prot |
-out |
Output database name | Path prefix |
-title |
Database title | String |
-parse_seqids |
Enable ID-based retrieval | Flag |
-taxid |
Assign taxonomy ID | Integer |
-taxid_map |
Taxonomy ID mapping file | Path |
What ships with it
1 file beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 1mo ago First seen · 354 lines · 45 tokens per session scan B 3725d0a4eb78
bio-local-blast is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 6mo ago), licensed MIT. It adds 45 tokens to every session and 3,093 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it B with 2 findings (asks for root, runs shell commands). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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