Use ViennaRNA Online

ViennaRNA Package 2.0: High-Performance RNA Secondary Structure Prediction

Predict RNA secondary structures and model molecular thermodynamics with unmatched computational speed and reliability. Built on the authoritative Turner 2004 energy parameters, ViennaRNA 2.0 provides an extensive suite of core algorithms for single-sequence analysis, comparative genomics, and RNA-RNA interactions.

Why ViennaRNA?

Secondary structure provides a vital, evolutionary conserved level of description for nucleic acids, encapsulating the dominant part of folding energy. Modeling these structures allows researchers to efficiently explain experimental findings and assess molecular thermodynamics without the burden of atom-scale, 3D spatial complexities.

The ViennaRNA Package 2.0 offers a major technical overhaul of the standard RNAlib core library and interactive command-line programs, optimizing your workflows for modern multi-core processors.

• Exceptional Prediction Accuracy: Benchmarks demonstrate superior predictive sensitivity and specificity over alternative tools like RNAstructure and UNAFold.

• Parallel Computing via OpenMP: Native support for concurrent computations on shared-memory multi-core systems, ensuring high-throughput data processing without speed bottlenecks.

• Diverse Algorithm Suite: Access everything from exact dynamic programming for ground states to partition functions, base pairing probabilities, and thermodynamic properties.

• Seamless Integration: Fully compliant with GNU standard command-line options and designed to handle stream-based input/output (UNIX pipes) for rapid pipeline construction.

Core Capabilities & Features

1. RNA Folding & Suboptimal Structures

• RNAfold: Computes minimum free energy (MFE) structures, partition functions, base pairing probability matrices, and centroid structures. Supports circular RNAs and user-supplied structural constraints.

• RNAsubopt: Generates comprehensive sets of suboptimal structures within specific energy bands, or delivers Boltzmann-weighted random samples via stochastic backtracking.

• Local Folding (Scanning): Run RNALfold and RNAplfold to scan genome-scale data for locally stable secondary structures and calculate local single-stranded accessibilities.

2. Advanced RNA-RNA Interactions

Evaluate molecular hybridization with unparalleled detail using specialized deployment modes:

• RNAup & RNAcofold: Calculate local opening energies and complex single or multi-site interactions between regulatory and target RNAs.

• RNAPKplex: Explicitly predicts pseudo-knotted RNA structures through optimized accessibility modeling.

• RNAplex: Achieves massive speed gains for large-scale target searches using an affine gap cost model for interior loops.

3. Comparative & Alignment Analysis

• RNAalifold: Compute global consensus structures in both MFE and partition function modes directly from multiple sequence alignments.

• Robust Scoring: Integrates thermodynamic parameters with sequence covariation, featuring support for the RIBOSUM substitution scoring scheme.

4. Interactive Utilities & Custom Parameterization

• Expanded Formats: Full native support for FASTA files, Clustal alignments, and STOCKHOLM layout structures (*.stk).

• Customizable Physics Tables: Swap the standard Turner 2004 parameters easily with human-readable text files—including pre-packaged Trained Andronescu parameters or specialized DNA folding databases.

Technical Specifications

The core routines are written as an ultra-fast, thread-safe C/C++ library (RNAlib). ViennaRNA achieves an optimal asymptotic time complexity of O(n^3) for standard thermodynamic modeling.

What is Tamarind Bio?

Tamarind Bio provides a next-generation web platform that simplifies complex computational biology workflows. By wrapping command-line bioinformatic utilities into scalable, high-performance web applications, Tamarind Bio enables structural biologists and researchers to run advanced prediction and modeling tasks directly from a browser without local hardware limitations or complex dependencies management.

How to Use ViennaRNA on Tamarind Bio

Running your RNA thermodynamic analyses using ViennaRNA on Tamarind Bio requires only a few straightforward steps:

1. Select Your Tool: Choose your desired configuration mode from the ViennaRNA interface (e.g., Global Folding with RNAfold or Local Scanning with RNALfold).

2. Upload Input Data: Paste or upload your sequence data in FASTA, Clustal, or Stockholm format.

3. Configure Parameters: Choose your structural parameters, such as applying custom dangling-end models, imposing base-pair constraints, or selecting between RNA and DNA folding energy parameters.

4. Run and Visualize: Click submit to process your queue in parallel via OpenMP. Downstream post-processing automatically renders human-readable outputs, including dot-bracket structure notation, centroid models, free energy estimates, and downloadable PostScript plots.

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