RNAduplex computes the hybridization structure between two RNA strands by predicting only intermolecular base pairs. Given two RNA sequences, it identifies optimal binding sites and calculates the hybridization free energy.
The program belongs to the ViennaRNA Package and uses the "interaction-only" (IO) approach: it models duplex formation without considering how intramolecular folding within each strand might compete with hybridization. This simplification makes RNAduplex extremely fast, operating at speeds comparable to sequence alignment while providing more information than simple BLAST searches. The tradeoff is that it may overestimate binding stability for sequences with stable internal structures.
RNAduplex works well for:
ProteinIQ provides cloud-hosted access to RNAduplex with no software installation required.
| Input | Description |
|---|---|
RNA Sequence 1 | First RNA sequence in FASTA format or plain nucleotides |
RNA Sequence 2 | Second RNA sequence to test for hybridization |
Supported file formats: .fasta, .fa, .txt
| Setting | Description |
|---|---|
Temperature | Folding temperature in degrees Celsius (0-100, default 37). Higher temperatures generally destabilize base pairing. |
Results display in spreadsheet format with the following columns:
| Column | Description |
|---|---|
Interaction | Identifier for the sequence pair |
Seq 1 Length | Length of the first RNA sequence |
Seq 2 Length | Length of the second RNA sequence |
Duplex Structure | Dot-bracket notation showing base pairs, with & separating the two strands |
Energy (kcal/mol) | Hybridization free energy. More negative values indicate stronger binding. |
Start (Seq1) | Starting position of the interaction on sequence 1 |
Start (Seq2) | Starting position of the interaction on sequence 2 |
The output uses dot-bracket notation with an ampersand separating the strands:
1.(((((.(((...((((((((((.&)))))))))))))))))).. indicates unpaired nucleotides( and ) indicate paired bases (matching pairs face each other across the &)& marks the boundary between the two sequencesRNAduplex uses dynamic programming to find the minimum free energy (MFE) configuration of intermolecular base pairs. The algorithm considers:
The calculation deliberately excludes intramolecular structure formation. Each nucleotide can participate in at most one intermolecular base pair, but neither strand folds onto itself during the prediction.
Because RNAduplex only considers intermolecular pairs, it does not account for:
For more accurate predictions that include these effects, follow up RNAduplex hits with RNAcofold (full dimer folding including intramolecular pairs) or RNAup (adds accessibility costs to the calculation).