bio-rna-structure-structure-probing
Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucleotide reactivity profiles that constrain structure prediction. Use when processing SHAPE-MaP or DMS-MaPseq sequencing data to obtain experimental RNA structure information.
npx skills add BioTender-max/awesome-bio-agent-skills --skill structure-probing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to 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 the
- Version Compatibility
- Platform Note
- ShapeMapper2 Pipeline
- Basic SHAPE-MaP Analysis
- With Denatured Control
- Amplicon Mode (Targeted)
- Key ShapeMapper2 Options
- ShapeMapper2 Output Files
- Reactivity Interpretation
- SHAPE Reactivity Scale
- Quality Filters
- Structure-Guided Folding with SHAPE Data
- RNAfold with SHAPE Constraints
- Python: SHAPE-Constrained Folding
Docker docker pull shapemapper2/shapemapper2 docker run -v $(pwd):/data shapemapper2/shapemapper2 shapemapper \ Singularity singularity pull shapemapper2.sif docker://shapemapper2/shapemapper2 singularity exec -B $(pwd):/data shapemapper2.sif shapemapper \ shapemapper \ For PCR-amplified targets Use ShapeMapper2 .shape output directly with RNAfold RNAfold --shape=results/my_rna_map.shape < target_rna.fa
What does the bio-rna-structure-structure-probing skill do?
Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucleotide reactivity profiles that constrain structure prediction. Use when processing SHAPE-MaP or DMS-MaPseq sequencing data to obtain experimental RNA structure information.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill structure-probing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.