RNA Secondary Structure Predictor

Predict RNA secondary structure using Nussinov algorithm. Calculate minimum free energy (MFE), dot-bracket notation, and visualize base pairs with circular arc diagram.

RNA Secondary Structure

0.0
MFE Score
0.0
ΔG (kcal/mol)
0
Base Pairs
0
GC Pairs
0
AU Pairs
0
GU Pairs
0
Stems
0
Unpaired

Dot-Bracket Notation

Annotated Sequence
 
What is RNA Secondary Structure?
RNA secondary structure is the set of base pairs that form when an RNA molecule folds on itself. These structures include stems (consecutive base pairs), loops, bulges, and junctions. Understanding RNA folding is crucial for predicting function in ribozymes, riboswitches, and regulatory elements.
How to Use This Tool
Quick guide to predict structure:
  1. Enter your RNA or DNA sequence (T converts to U)
  2. Set minimum loop size (3-5 recommended)
  3. Choose whether to allow G-U wobble pairs
  4. Click "Predict Structure"
  5. View MFE, dot-bracket notation, and circular diagram
Applications
This tool is useful for:
  • mRNA structure prediction
  • Riboswitch identification
  • miRNA precursor analysis
  • Ribozyme active site prediction
  • RNA vaccine design
  • Antisense oligonucleotide design
Nussinov Algorithm
The Nussinov algorithm uses dynamic programming to find the maximum number of base pairs in RNA secondary structure. It considers Watson-Crick pairs (GC, AU) and optionally G-U wobble pairs. The MFE score represents the maximum number of base pairs found (higher = more stable).
Understanding Results
Result components explained:
  • MFE Score: Maximum base pairs found
  • Dot-Bracket: ( ) for pairs, . for unpaired
  • Annotated Sequence: Color-coded bases
  • Circular Diagram: Arc visualization of pairs
  • Stems: Consecutive base pairs
FAQ
Q: What's the minimum loop size?
A: Typically 3 nucleotides. Smaller loops are sterically unfavorable.
Q: Should I allow G-U wobble pairs?
A: Yes, G-U pairs are common in RNA and stabilize structures, though weaker than Watson-Crick pairs.