Enter RNA Folding Inputs
Example Data Table
| Sample | Sequence Length | GC Content | Predicted Pairing Rate | MFE Proxy | Structure Class |
|---|---|---|---|---|---|
| miRNA-like fragment | 24 nt | 50.00% | 58.33% | -6.80 kcal/mol | Moderately structured |
| GC-rich stem candidate | 30 nt | 66.67% | 73.33% | -13.45 kcal/mol | Highly structured |
| Loop-heavy test strand | 27 nt | 40.74% | 37.04% | -2.65 kcal/mol | Lightly structured |
These rows are illustrative examples showing how the output may look under typical settings.
Formula Used
This calculator uses a weighted Nussinov-style dynamic programming model. It rewards valid base pairs and finds a non-crossing structure that maximizes total pairing score under your minimum loop setting.
Weighted pair score: GC pairs use the strongest score, AU pairs use a medium score, and optional GU wobble pairs use a lighter score.
MFE proxy: Pair energy + stacking bonus + loop penalties + temperature adjustment + salt adjustment.
Pair energy proxy: (GC pairs × -3.4) + (AU pairs × -2.1) + (GU pairs × -1.0).
Stacking bonus: -0.45 × stacked pairs × stacking factor.
Loop penalties: Hairpins × 1.90, internal loops × 1.30, bulges × 0.90, all scaled by your loop penalty factor.
Temperature adjustment: 0.025 × (temperature - 37) × predicted base pairs.
Salt adjustment: -0.08 × ln(1 + 10×Na + 120×Mg) × predicted base pairs.
This is an explainable classroom and screening heuristic, not a replacement for full thermodynamic folding software or laboratory validation.
How to Use This Calculator
- Enter a label so exported reports are easier to identify.
- Paste an RNA sequence using A, U, C, and G characters.
- Set temperature, sodium, magnesium, and the minimum loop size.
- Adjust GC, AU, and GU weights if you want custom scoring.
- Change stacking and loop penalty factors for sensitivity testing.
- Enable GU wobble if your biological context supports it.
- Press Predict Structure to view the result above the form.
- Review the dot-bracket notation, stability signals, and export buttons.
Frequently Asked Questions
1. What does the dot-bracket output show?
Dots mark unpaired nucleotides. Opening and closing brackets mark paired bases. This gives a compact view of the predicted secondary structure pattern.
2. Is this the same as a full RNA folding engine?
No. This calculator uses a weighted heuristic dynamic program for fast prediction. It is useful for screening, teaching, and comparative analysis, not final structure confirmation.
3. Why does the MFE proxy become less negative?
Less negative values suggest weaker apparent stabilization. Fewer strong pairs, more loops, higher temperatures, or weaker salt conditions can push the estimate upward.
4. Why can GU wobble pairing matter?
Some RNA structures tolerate GU wobble pairs. Enabling them can increase possible stems and alter the final dot-bracket pattern, especially in loop-rich sequences.
5. What sequence length works best here?
Short and moderate sequences work best because the browser must solve a dynamic program. The tool caps input at 150 nucleotides for responsive performance.
6. Can I paste DNA instead of RNA?
Yes, but any T character is converted to U automatically. That lets you test RNA-like folding tendencies from a DNA-style sequence entry.
7. How should I interpret the stability index?
It summarizes pairing density, GC richness, and normalized energy into one quick score. Higher values generally indicate a more stable predicted fold under your settings.
8. What do the CSV and PDF exports contain?
Both exports include the label, cleaned sequence, structural metrics, energy proxy, confidence score, class label, and dot-bracket notation for easy sharing.