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 PKU-YuanGroup/OpenAI4S --skill bio-database-access-local-blastgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote 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/pku-yuangroup/openai4s/bio-database-access-local-blast)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-database-access-local-blast"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/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/pku-yuangroup/openai4s/bio-database-access-local-blast"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/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 | $0.00116 | $0.04783 |
| Opus 5 | $0.00058 | $0.02391 |
| Sonnet 5 | $0.00023 | $0.00957 |
| Haiku 4.5 | $0.00012 | $0.00478 |
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 9d 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.
out = subprocess.run([name, '-version'], capture_output=True, text=True) This is a copy
98% identical to bio-local-blast — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 385 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:
- CLI:
blastn -versionthenblastn -helpto confirm flags - CLI:
makeblastdb -helpto confirm database build options
If a flag is unrecognized or behavior changes, introspect with -help and adapt the example to match the installed version rather than retrying.
Local BLAST
"Run BLAST locally for speed and control" -> Build or download a BLAST+ database, run the appropriate program with carefully chosen -task, masking, and thread settings, parse tabular output. Local BLAST is the right tool when remote is rate-limited or when the database must be reproducible (frozen).
The biggest mistakes are (a) using nt/nr without realizing they're >250 GB and grow weekly, (b) not building with -parse_seqids and then being unable to extract hit sequences with blastdbcmd, (c) using default blastn for cross-species when dc-megablast is correct, and (d) thinking -num_threads 32 will scale -- past ~16 threads BLAST is I/O bound.
- CLI:
makeblastdb,blastn/blastp,blastdbcmd,update_blastdb.pl(NCBI BLAST+) - Python:
subprocesswrapper (preferred);Bio.Blast.Applicationswas deprecated and removed -- do not use
Installation
# conda (preferred)
conda install -c bioconda blast
# macOS
brew install blast
# Ubuntu
sudo apt install ncbi-blast+
# Verify
blastn -version # NCBI BLAST+ 2.15+ expected
update_blastdb.pl --showall pretty | head
Database format: v5 vs v4
NCBI introduced BLAST database v5 in BLAST+ 2.10 (2020). v5 includes taxonomy indexing directly in the database files, enabling -taxids and -taxidlist filtering without a companion file. v4 databases require taxonomy4blast.sqlite3 to be present and discoverable.
| Feature | v4 | v5 |
|---|---|---|
| Default for prebuilt NCBI dbs | No (legacy) | Yes (since 2020) |
-taxids, -taxidlist support |
No | Yes |
blastdbcmd -taxids |
No | Yes |
New -info output fields |
No | Yes |
What ships with it
5 files 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.
- 9d ago First seen · 385 lines · 116 tokens per session scan B e5c8078ed0a9
bio-local-blast is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 116 tokens to every session and 4,783 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it B with 2 findings (asks for root, runs shell commands). It is 98% identical to bio-local-blast, differing in 12 lines, and is treated as a copy.
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