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-blast-searchesgit 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-blast-searches)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-database-access-blast-searches"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-database-access-blast-searches/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-blast-searches"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-database-access-blast-searches.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 | $0.00130 | $0.04334 |
| Opus 5 | $0.00065 | $0.02167 |
| Sonnet 5 | $0.00026 | $0.00867 |
| Haiku 4.5 | $0.00013 | $0.00433 |
Grade A, and why
bio-blast-searches scanned grade A with 0 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
This is a copy
98% identical to bio-blast-searches — 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 — 319 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: BioPython 1.83+, NCBI BLAST+ 2.15+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show biopythonthenhelp(Bio.Blast.NCBIWWW.qblast)to check signatures - CLI:
blastn -versionthenblastn -help
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
BLAST Searches (Remote)
"Find similar sequences in NCBI's database" -> Submit a query to NCBI's remote BLAST servers; receive a Request ID (RID); poll for completion; parse the XML hit table. Best for one-off identification of a few sequences. For >50 sequences, switch to local-blast or DIAMOND/MMseqs2 in remote-homology.
The two most consequential decisions: which program (defines query+target molecule types and word-size defaults) and which database (defines the search space and therefore E-value baselines). The third most important: do NOT misuse max_target_seqs -- it is an early-termination heuristic, not a "give me the top N hits" filter (Shah et al. 2019).
- Python:
NCBIWWW.qblast(program, db, sequence)+NCBIXML.read(handle)(BioPython) - CLI:
blastn -remote -db nt -query seq.fa -out hits.xml -outfmt 5(BLAST+) - Web: https://blast.ncbi.nlm.nih.gov/Blast.cgi (RID lookup)
Required Setup
from Bio.Blast import NCBIWWW, NCBIXML
from Bio import SeqIO
No API key needed for remote BLAST itself, but NCBI's general rate-limit ethic still applies -- one search at a time, polite waiting, no parallelism.
Program decision (query vs database molecule)
| Program | Query | Target | Word size default | Use case |
|---|---|---|---|---|
blastn |
DNA | DNA | 11 | General DNA similarity |
megablast |
DNA | DNA | 28 | High-identity DNA (>=95%) -- PCR primer hits, contamination |
dc-megablast |
DNA | DNA | 11 (discontiguous) | Cross-species mRNA (sensitive, gapped) |
blastp |
Protein | Protein | 3 (6 also valid) | General protein homology |
blastx |
DNA | Protein | 3 | Translated DNA query vs protein DB; ORF discovery |
tblastn |
Protein | DNA | 3 | Protein query vs translated DB; find unannotated CDS |
tblastx |
DNA | DNA | 3 (both translated) | Most expensive; deep cross-species coding similarity |
psiblast |
Protein | Protein | 3 | Iterative PSSM-based remote homology -- see remote-homology |
What ships with it
4 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 · 319 lines · 130 tokens per session scan A 87f74ebe1aa1
bio-blast-searches is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 130 tokens to every session and 4,334 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it A with 0 findings. It is 98% identical to bio-blast-searches, differing in 12 lines, and is treated as a copy.
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