C. elegans Feeding RNAi
Design and score L4440 feeding RNAi in C. elegans.
Overview
Problem. Need clonable primer pairs and a quality-scored target.
Use when: Doing C. elegans feeding RNAi
Avoid when: Other species or methods
Learning goals
- What a species-specific workflow looks like
- Design and evaluation are two sides of one coin
Figures
Tutorial
Overview
This skill covers two tightly related workflows for C. elegans feeding RNAi using the L4440 vector system:
| Function | Trigger phrase examples | Key output |
|---|---|---|
| design | "design RNAi for daf-2", "帮我设计 kynu-1 的 RNAi 引物" | Primer CSV + gene-structure SVG + chat summary |
| evaluate | "evaluate this RNAi sequence for daf-16", "评价这段 RNAi 序列的效果" | Evaluation report CSV + chat summary |
Function 1 — design
When to invoke
User provides a C. elegans gene name (or WormBase Gene ID) and asks to design, create, or generate an RNAi construct / primers.
Required inputs
- Gene name (e.g.
kynu-1,daf-2) or WormBase Gene ID (e.g.WBGene00002264)
Optional parameters (ask if not specified)
| Parameter | Default | Description |
|---|---|---|
n_candidates |
3 | Number of non-redundant target regions to return |
target_length |
200 bp | Sliding-window size for target region screening |
gc_min / gc_max |
40 / 60 % | GC content filter for candidate regions |
Outputs
{gene}_RNAi_primers.csv— saved to/mnt/results/{gene}_target_region.svg— gene structure diagram, saved to/mnt/results/- Chat summary — top candidate primer sequences, key QC metrics, cloning note
Implementation
See impl.md → Section A (Design Module).
Function 2 — evaluate
When to invoke
User provides a C. elegans gene name plus an existing RNAi sequence (target region DNA or primer pair) and asks to assess, score, or evaluate it.
Required inputs
- Gene name or WormBase Gene ID
- RNAi sequence in one of two formats (auto-detected):
- Target region sequence: ~200 bp DNA string (no RE adapters)
- Primer pair: Forward + Reverse primer sequences (RE adapters stripped automatically)
Outputs
{gene}_RNAi_evaluation.csv— detailed scores, saved to/mnt/results/- Chat evaluation report — Markdown table with four dimension scores + overall recommendation
Implementation
See impl.md → Section B (Evaluate Module).
Shared Constraints
- Organism: C. elegans only (NCBI taxid 6239)
- Vector: L4440 with HindIII (forward adapter
CCCAAGCTT) + SalI (reverse adapterGGGGTCGAC) - BLAST: uses NCBI remote service; requires network access
- Runtime: ~2–5 min per gene (BLAST is the bottleneck)
- Machine: default
worker-0is sufficient (< 100 MB RAM)
Code preview
No Python/R preview files were found.
Companion files
| Type | Path | Bytes |
|---|---|---|
| Markdown | impl.md | 14,067 |
| Markdown | SKILL.md | 2,543 |
| JSON | skill.meta.json | 877 |