bio-genome-annotation-ncrna-annotation
Identify non-coding RNAs including tRNAs, rRNAs, snoRNAs, and regulatory RNAs using Infernal covariance model searches against Rfam and tRNAscan-SE for tRNA prediction. Use when performing genome-wide ncRNA annotation with assembly input producing GFF output.
npx skills add BioTender-max/awesome-bio-agent-skills --skill ncrna-annotation --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: 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. # Non-Coding RNA Annotation **"Find non-coding RNAs in my genome"** → Scan a genome assembly for rRNAs, tRNAs, snoRNAs, and other ncRNA families using covariance model search and specialized detectors. - CLI: `cmscan --rfam --tblout hits.tbl Rfam.cm assembly.fa` (Infernal), `tRNAscan-SE -o trnas.txt assembly.fa` Identify and annotate non-coding RNAs in genome assemblies using Infernal (general ncRNAs via Rfam covariance models) and tRNAscan-SE (specialized tRNA detection). ## Infernal / cmscan Infernal uses covariance models (CMs) from Rfam to identify ncRNA families by both sequence and secondary structure similarity. ### Rfam Database Setup ```bash # Download Rfam covariance models (~600 MB compressed) wget https://ftp.ebi.ac.uk/pub/da
- Version Compatibility
- Infernal / cmscan
- Rfam Database Setup
- Basic cmscan
- Key Options
- Convert cmscan Output to GFF3
- E-value Guidelines
- tRNAscan-SE
- Basic Usage
- Domain-Specific Models
- Expected tRNA Counts
- barrnap (rRNA Detection)
- Combining ncRNA Annotations
- Troubleshooting
Download Rfam covariance models (~600 MB compressed) wget https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz gunzip Rfam.cm.gz Press the CM database (required for cmscan) cmpress Rfam.cm Download clan information (for overlap resolution) wget https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.clanin Search genome against all Rfam families cmscan \ Rfam.cm \
What does the bio-genome-annotation-ncrna-annotation skill do?
Identify non-coding RNAs including tRNAs, rRNAs, snoRNAs, and regulatory RNAs using Infernal covariance model searches against Rfam and tRNAscan-SE for tRNA prediction. Use when performing genome-wide ncRNA annotation with assembly input producing GFF output.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill ncrna-annotation --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.