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 agentmods add skills/thesecondfox/skill/bio-rna-structure-structure-probingnpx skills add thesecondfox/skill --skill bio-rna-structure-structure-probinggit 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-structure-probing)<a href="https://agentmods.dev/skills/thesecondfox/skill/bio-rna-structure-structure-probing"><img src="https://agentmods.dev/badge/skills/thesecondfox/skill/bio-rna-structure-structure-probing.svg" alt="Measured on agentmods" 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 | $0.03308 |
| Opus 5 | $0.00037 | $0.01654 |
| Sonnet 5 | $0.00015 | $0.00662 |
| Haiku 4.5 | $0.00007 | $0.00331 |
Grade A, and why
bio-rna-structure-structure-probing 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 2d 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 — 347 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: STAR 2.7.11+, eggNOG-mapper 2.1+, matplotlib 3.8+, numpy 1.26+, 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.
Structure Probing
"Process my SHAPE-MaP experiment to get RNA reactivity profiles" → Convert mutation rates from SHAPE-MaP or DMS-MaPseq sequencing data into per-nucleotide reactivity profiles, then use reactivities as constraints for thermodynamic structure prediction.
- CLI:
shapemapper(ShapeMapper2) for end-to-end SHAPE-MaP processing - CLI:
RNAfold --shape(ViennaRNA) for SHAPE-constrained folding
Analyze experimental RNA structure probing data (SHAPE-MaP, DMS-MaPseq) to obtain per-nucleotide reactivity profiles. High reactivity indicates flexible/single-stranded nucleotides; low reactivity indicates base-paired/structured positions. Reactivities constrain thermodynamic folding for more accurate structure prediction.
Platform Note
ShapeMapper2 is Linux-only. On macOS, use Docker or Singularity:
# Docker
docker pull shapemapper2/shapemapper2
docker run -v $(pwd):/data shapemapper2/shapemapper2 shapemapper \
--target /data/target.fa --modified --R1 /data/mod_R1.fq.gz --R2 /data/mod_R2.fq.gz \
--untreated --R1 /data/unmod_R1.fq.gz --R2 /data/unmod_R2.fq.gz \
--out /data/results
# Singularity
singularity pull shapemapper2.sif docker://shapemapper2/shapemapper2
singularity exec -B $(pwd):/data shapemapper2.sif shapemapper \
--target /data/target.fa --modified --R1 /data/mod_R1.fq.gz ...
ShapeMapper2 Pipeline
Basic SHAPE-MaP Analysis
shapemapper \
--target target_rna.fa \
--name my_rna \
--modified --R1 modified_R1.fastq.gz --R2 modified_R2.fastq.gz \
--untreated --R1 untreated_R1.fastq.gz --R2 untreated_R2.fastq.gz \
--out results/ \
--nproc 8 \
--min-depth 5000
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.
- 2d ago First seen · 347 lines · 75 tokens per session scan A a45af5840a51
bio-rna-structure-structure-probing 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 3,308 once invoked, about $0.0004 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 2026-09-03.
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