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tooluniverse-noncoding-rna
Non-coding RNA analysis — miRNAs (miRBase, miRDB targets), lncRNAs (LNCipedia, RNAcentral), circRNAs, snoRNAs, and other ncRNA classes. Distinct mechanisms per class — miRNAs repress mRNA; lncRNAs scaffold/decoy/enhance. Use for ncRNA function prediction, miRNA-target prediction, lncRNA functional annotation, and ncRNA-disease association queries.
skills/tooluniverse-noncoding-rna/SKILL.md
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# Non-Coding RNA Analysis
Pipeline for identifying, annotating, and interpreting non-coding RNAs and their biological roles. Covers microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and other ncRNA classes.
**Key principles**:
1. **Class determines function** — miRNAs repress mRNA translation; lncRNAs have diverse mechanisms (scaffolds, guides, decoys, enhancers); rRNAs/tRNAs are structural
2. **Targets matter more than the ncRNA itself** — for miRNAs, the regulated mRNA targets determine the phenotype
3. **Expression context is critical** — ncRNAs are highly tissue/cell-type specific
4. **Conservation indicates function** — deeply conserved ncRNAs (miR-let-7, MALAT1) have well-established roles
5. **Evidence grading** — T1: validated targets (reporter assay, CLIP-seq), T2: high-confidence computational prediction, T3: expression correlation, T4: sequence-based prediction only
**Type-based reasoning — look up, don't guess**:
Non-coding RNA function depends on type: miRNA silences target mRNAs (look up targets in miRTarBase/TargetScan), lncRNA has diverse functions (scaffolding, guiding, decoying — check literature for the specific lncRNA), circRNA may sponge miRNAs.
