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-rna-structure-ncrna-searchgit 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-rna-structure-ncrna-search)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-rna-structure-ncrna-search"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-rna-structure-ncrna-search/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-rna-structure-ncrna-search"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-rna-structure-ncrna-search.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 | $0.00075 | $0.02245 |
| Opus 5 | $0.00037 | $0.01123 |
| Sonnet 5 | $0.00015 | $0.00449 |
| Haiku 4.5 | $0.00007 | $0.00225 |
Grade A, and why
bio-rna-structure-ncrna-search scanned grade A with 1 finding 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 8d 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.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
wget https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz How it starts
The opening of the file, as written. The whole thing — 247 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+, Infernal 1.1+, pandas 2.2+
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.
ncRNA Search
"Search my sequences for known non-coding RNA families" → Query sequences against the Rfam database using covariance models that score both sequence and secondary structure conservation, or build custom CMs for novel RNA families.
- CLI:
cmscanfor searching against Rfam CMs - CLI:
cmbuild+cmcalibratefor building custom covariance models
Search for non-coding RNA homologs and classify RNA families using covariance models (CMs). Infernal scores both sequence and secondary structure conservation, making it more sensitive than sequence-only methods for structured RNAs.
Rfam Database Setup
# Download current Rfam covariance models (~500 MB compressed)
wget https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz
gunzip Rfam.cm.gz
# Press the CM database (required before searching)
cmpress Rfam.cm
# Download clan information (for resolving overlapping hits)
wget https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.clanin
cmscan: Query Sequences Against Rfam
Search one or more query sequences against the full Rfam database to classify ncRNAs by family.
# Basic cmscan against Rfam
cmscan --cpu 8 --tblout results.tbl --fmt 2 Rfam.cm query.fa > results.out
# With clan overlap resolution (removes redundant hits from same clan)
cmscan --cpu 8 --tblout results.tbl --fmt 2 --clanin Rfam.clanin --oclan Rfam.cm query.fa > results.out
# Strict E-value threshold for high-confidence hits
cmscan --cpu 8 --tblout results.tbl --fmt 2 --clanin Rfam.clanin --oclan \
-E 1e-5 --incE 1e-5 Rfam.cm query.fa > results.out
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.
- 8d ago First seen · 247 lines · 75 tokens per session scan A e8133d4d791f
bio-rna-structure-ncrna-search is a skill published in the GitHub repository thesecondfox/skill (3 stars, last pushed 5mo ago), licensed MIT. It adds 75 tokens to every session and 2,245 once invoked, about $0.0004 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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