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 fmschulz/omics-skills --skill bio-fasta-database-curatorgit clone --depth 1 https://github.com/fmschulz/omics-skillsWrote 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/fmschulz/omics-skills/bio-fasta-database-curator)<a href="https://agentmods.dev/skills/fmschulz/omics-skills/bio-fasta-database-curator"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-fasta-database-curator/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/fmschulz/omics-skills/bio-fasta-database-curator"><img src="https://agentmods.dev/badge/skills/fmschulz/omics-skills/bio-fasta-database-curator.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 | $0.00052 | $0.02157 |
| Opus 5 | $0.00026 | $0.01078 |
| Sonnet 5 | $0.00010 | $0.00431 |
| Haiku 4.5 | $0.00005 | $0.00216 |
Grade A, and why
bio-fasta-database-curator 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 3d 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.
How it starts
The opening of the file, as written. The whole thing — 261 lines — stays where its author put it; the contents beside it link to each section on GitHub.
FASTA Database Curator
Overview
Automate the curation and standardization of biological sequence databases. This skill handles the tedious work of processing FASTA/FAA files, ensuring consistent header formats, removing duplicates, and preparing databases for downstream analysis.
Supplementary version-grounded tool notes: tools.md.
Key Capabilities:
- Header format standardization (pipe separators, prefixes)
- Duplicate detection and removal (by sequence or ID)
- Format conversion (GenBank → FASTA, multi-line → single-line)
- Database merging with conflict resolution
- Statistics generation (counts, lengths, taxonomy, GC content)
- Validation (no whitespace in headers, proper formatting)
- Taxonomy label extraction and standardization
When to Use This Skill
Use this skill when:
- User needs to standardize sequence headers
- User wants to merge multiple FASTA files
- User needs to remove duplicate sequences
- User is preparing a database for HMM/BLAST/MMseqs2
- User wants database statistics and quality metrics
- User needs to convert between sequence formats
Header Format Standards
Recommended Format
Use pipe-separated fields with consistent prefixes:
>PREFIX|ACCESSION|DESCRIPTION
SEQUENCE...
Examples:
>VP|Mavirus_MCP|Major capsid protein [Virophage]
>PLV|NC_021333_1|Polinton-like virus hypothetical protein
>NCLDV|YP_009173877.1|DNA polymerase [Marseilleviridae]
Common Transformations
# Remove whitespace from headers
old: ">VP_MCP Mavirus major capsid protein"
new: ">VP_MCP|Mavirus_major_capsid_protein"
# Add taxonomy prefix
old: ">NC_021333.1 hypothetical protein"
new: ">PLV|NC_021333.1|hypothetical_protein"
# Standardize separators
old: ">seq1 [organism=Virus] protein"
new: ">seq1|Virus|protein"
Quick Reference
| Task | Action |
|---|---|
| Inspect database | Count records, sample headers, check whitespace and length distribution before changing anything. |
| Standardize headers | Define deterministic transformation rules and preserve original-to-new ID mapping. |
| Merge or deduplicate | Decide whether duplicates are removed by ID, sequence, or both, then report what changed. |
| Validate output | Re-count records, verify FASTA syntax, and write database statistics. |
| Run the bundled curator | uv run --script skills/bio-fasta-database-curator/scripts/curate_fasta.py input.fasta --output curated.fasta --prefix REF --deduplicate both |
What ships with it
3 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.
- 3d ago Changed 282dd87ebaae
- 9d ago First seen · 261 lines · 52 tokens per session scan A 47bcbc6a6578
bio-fasta-database-curator is a skill published in the GitHub repository fmschulz/omics-skills (7 stars, last pushed 4d ago), licensed MIT. It adds 52 tokens to every session and 2,157 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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