bio-genome-annotation-functional-annotation
Assign GO terms, KEGG orthologs, Pfam domains, and EC numbers to predicted proteins using eggNOG-mapper and InterProScan. Produces functional summaries for downstream pathway and enrichment analysis. Use when adding functional annotation to predicted genes or characterizing protein functions in a new genome.
npx skills add BioTender-max/awesome-bio-agent-skills --skill functional-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. # Functional Annotation **"Functionally annotate my predicted proteins"** → Assign GO terms, KEGG orthologs, Pfam domains, and EC numbers to predicted protein sequences using orthology-based and domain-scan methods. - CLI: `emapper.py -i proteins.fa --output annotations` (eggNOG-mapper), `interproscan.sh -i proteins.fa` (InterProScan) Assign functional annotations (GO terms, KEGG orthologs, Pfam domains, EC numbers) to predicted protein sequences using eggNOG-mapper and InterProScan. ## eggNOG-mapper ### Database Setup ```bash # Download eggNOG v5.0 database (~44 GB) # Required for local searches; use --data_dir to specify location download_eggnog_data.py --data_dir /path/to/eggnog_db -y # Download DIAMOND database only (~9 GB, faster se
- Version Compatibility
- eggNOG-mapper
- Database Setup
- Basic Usage
- Key Options
- With Taxonomic Scope
- Output Files
- Key Output Columns
- InterProScan
- Select Specific Databases
- Available Applications
- Merging eggNOG and InterProScan Results
- Annotation Statistics
- Troubleshooting
Download eggNOG v5.0 database (~44 GB) Required for local searches; use --data_dir to specify location download_eggnog_data.py --data_dir /path/to/eggnog_db -y Download DIAMOND database only (~9 GB, faster setup) download_eggnog_data.py --data_dir /path/to/eggnog_db -y -D Download taxon-specific databases (optional, smaller) download_eggnog_data.py --data_dir /path/to/eggnog_db -y -t 2 # Bacteria download_eggnog_data.py --data_dir /path/to/eggnog_db -y -t 2759 # Eukaryota emapper.py \ Restrict to bacterial orthologs for a prokaryotic genome
What does the bio-genome-annotation-functional-annotation skill do?
Assign GO terms, KEGG orthologs, Pfam domains, and EC numbers to predicted proteins using eggNOG-mapper and InterProScan. Produces functional summaries for downstream pathway and enrichment analysis. Use when adding functional annotation to predicted genes or characterizing protein functions in a new genome.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill functional-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.