Related tools
RNAduplex
RNAduplex computes the hybridization structure between two RNA sequences. Predicts the optimal duplex formation and binding energy.
RNAup
RNAup predicts accessibility-aware RNA-RNA interactions, reporting opening-energy terms alongside interaction energies and downloadable upstream output files.
RNAcofold
RNAcofold predicts the joint secondary structure of two interacting RNA molecules and optionally reports partition-function and concentration-dependent equilibrium metrics.
RNAdistance
RNAdistance compares RNA secondary structures using the selected upstream ViennaRNA distance representation and comparison mode.
RNAdos
RNAdos calculates density-of-states summaries for RNA sequences, reporting representative structures and state counts across energy bands.
RNAeval
RNAeval calculates the free energy of an RNA secondary structure for a given sequence. Evaluates if a proposed structure is thermodynamically favorable.
RNAfold
RNAfold predicts RNA secondary structure using minimum free energy (MFE) algorithms and optionally returns partition-function ensemble metrics when explicitly enabled.
RNALfold
RNALfold reports locally stable RNA secondary structures within a sliding window and returns their start and end positions on the input sequence.
RNAplfold
RNAplfold computes local base pair probabilities using a sliding window approach. Useful for analyzing accessibility and identifying binding sites in long RNA sequences.
RNAplot
RNAplot renders ViennaRNA secondary-structure plot files from a supplied RNA sequence and dot-bracket structure.
What is RNAplex?
RNAplex predicts RNA-RNA interaction sites at high speed by combining precomputed accessibility profiles with a fast duplex scanning algorithm. It is designed for cases where a short query RNA (such as a miRNA, siRNA, or antisense oligo) needs to be scanned against a long target sequence (such as an mRNA transcript or genomic region) to locate potential binding sites.
The core idea behind RNAplex is a two-stage approach. First, accessibility information is computed for the target sequence using a local folding model similar to RNAplfold. Then, the algorithm scans for favorable interaction sites while incorporating these accessibility penalties. This makes RNAplex significantly faster than RNAup for long targets while still accounting for the structural context of each strand.
When to use RNAplex
RNAplex fills a specific niche in the ViennaRNA interaction toolkit:
- miRNA target prediction: scanning a full transcript for sites complementary to a 20-22 nt miRNA
- Antisense oligonucleotide design: identifying accessible regions on a long target RNA
- High-throughput screening: when many query-target pairs need to be evaluated quickly
- Genome-scale searches: situations where RNAup's per-pair computation time becomes prohibitive
For a single pair of short RNAs where accuracy matters more than speed, RNAup provides a more thorough accessibility calculation. RNAplex trades some precision for the ability to handle long sequences efficiently.
How to use RNAplex online
RNAplex on ProteinIQ accepts a target RNA and a query RNA, runs the ViennaRNA RNAplex program with optional accessibility scaling, and returns ranked interaction hits with coordinates, predicted structures, and energies. No local software installation is required.
Inputs
| Input | Description |
|---|---|
Target RNA | The longer RNA sequence to scan for interaction sites. FASTA or plain nucleotide format. |
Query RNA | The shorter RNA (e.g., miRNA) to search for binding sites. FASTA or plain nucleotide format. |
Supported file formats: .fasta, .fa, .txt
Settings
| Setting | Type | Default | Description |
|---|---|---|---|
Interaction length | text | upstream default | Maximum length of the predicted interaction region. Limits how many consecutive base pairs the algorithm considers. |
Energy threshold | text | upstream default | Only report interactions with free energy below this cutoff (in kcal/mol). Lower thresholds produce fewer, stronger hits. |
Duplex distance | text | upstream default | Minimum distance between reported interaction sites on the target. Prevents overlapping hits from cluttering the output. |
Scale accessibility | text | upstream default | Scaling factor applied to the accessibility penalty. A value of 0 disables accessibility correction entirely (pure duplex mode); higher values increase the penalty for structured regions. |
Window length | text | upstream default | Window size for the local accessibility computation. Larger windows consider more structural context but increase runtime. |
Temperature | slider (0-100) | 37 | Folding temperature in degrees Celsius. |
Salt concentration | text | upstream default | Monovalent salt concentration for the ViennaRNA energy model. |
Initial salt correction | text | upstream default | Initial salt correction parameter. |
Parameter file content | textarea | none | Inline ViennaRNA parameter file content passed via --paramFile. |
Leaving optional text fields blank preserves the upstream ViennaRNA CLI defaults.
Output
| Column | Description |
|---|---|
Interaction | Identifier for the query-target pair |
Query ID | Identifier of the query sequence |
Target ID | Identifier of the target sequence |
Query Start / Query End | Nucleotide positions of the interaction on the query strand |
Target Start / Target End | Nucleotide positions of the interaction on the target strand |
Structure | Dot-bracket notation of the predicted duplex, with & separating the two strands |
Energy (kcal/mol) | Predicted interaction energy. More negative values indicate stronger predicted binding. |
Results are sorted by energy, with the most favorable interactions listed first.
Speed vs. accuracy tradeoff
RNAplex sits between RNAduplex and RNAup in both speed and accuracy:
- RNAduplex is the fastest option but ignores all structural context, often overestimating binding strength
- RNAplex incorporates precomputed accessibility profiles, catching the most obvious structural barriers without the full per-site calculation
- RNAup computes opening energies from scratch for each interaction site, giving the most accurate decomposition at the cost of longer runtimes
For a typical workflow, start with RNAplex to identify candidate sites on a long target, then refine the top hits with RNAup for accurate energy decomposition.