RNALfold computes locally stable RNA secondary structures using a sliding window approach. Part of the ViennaRNA Package, it identifies regions within long sequences that can form stable hairpins, stems, and other structural motifs without requiring the entire sequence to fold cooperatively.
The algorithm scales linearly with sequence length when the window size is fixed, using O(n + L²) memory and O(n · L²) CPU time where n is sequence length and L is window size. This efficiency makes RNALfold practical for scanning entire chromosomes or genomes to identify structured elements.
RNALfold is designed for scenarios where global folding is inappropriate or computationally prohibitive:
RNALfold applies the Zuker minimum free energy algorithm within a sliding window. For each position in the sequence, it considers only base pairs where both partners fall within a window of the specified size. This constraint prevents unrealistic long-range pairings that would never form in a biological context.
The algorithm reports locally optimal structures: those that cannot be improved by small perturbations within their region. A structure is reported only if it represents a genuine local minimum in the energy landscape, filtering out suboptimal folds that would be outcompeted by nearby alternatives.
While RNALfold returns discrete structures (in dot-bracket notation), RNAplfold computes base pair probabilities across the ensemble of possible local structures. RNALfold answers "what is the most stable local structure here?" while RNAplfold answers "how likely is each position to be paired?"
For most applications involving target site accessibility or structural diversity, RNAplfold provides more informative output. RNALfold is better suited when specific structural predictions are needed.
ProteinIQ provides browser-based access to RNALfold, running computations on cloud infrastructure without requiring local installation of the ViennaRNA Package.
| Input | Description |
|---|---|
RNA Sequences | One or more RNA sequences in FASTA format or plain text. Supports very long sequences (up to 50 MB). |
| Setting | Description |
|---|---|
Window size | Maximum span of local structures (50-500, default 150). Larger values detect longer-range pairings but increase computation time. |
Temperature | Folding temperature in degrees Celsius (0-100, default 37). Affects thermodynamic stability calculations. |
Results are returned as a spreadsheet with multiple rows per input sequence (one per local structure found):
| Column | Description |
|---|---|
Sequence ID | Identifier from FASTA header or auto-generated |
Structure # | Index of the local structure within this sequence |
Length | Length of the local structure in nucleotides |
Local Structure | Dot-bracket notation showing the structure |
Energy | Free energy of the local structure in kcal/mol |
The window size parameter determines the maximum span of detectable structures:
| Window Size | Suitable For |
|---|---|
| 50-100 | Small hairpins, miRNA precursors |
| 100-200 | Typical regulatory elements, tRNAs |
| 200-300 | Larger riboswitches, some ribozymes |
| 300-500 | Complex structured domains |
Smaller windows run faster and produce more focused results. Larger windows can detect more complex structures but may report many overlapping alternatives.
RNALfold shares limitations common to ViennaRNA tools:
For very long sequences, the number of reported structures can be large. The output is limited to 50 structures per sequence to keep results manageable.
