ViennaRNA Package 2.0

TLDR

RNA secondary structure is a key, evolutionarily conserved descriptor of nucleic acids, and the ViennaRNA Package has been a widely used tool for nearly twenty years to analyze it. The authors aimed to overhaul the ViennaRNA Package to accommodate updated energy models, multi‑core CPU support, and new algorithmic variants. They reimplemented RNAlib and user programs with dynamic‑programming‑based tools for RNA‑RNA interactions, restricted ensembles, centroid and maximum expected accuracy structures, z‑scores, and fasta input, while preserving core algorithm efficiency and backward compatibility. ViennaRNA Package 2.0, which supports OpenMP parallelism, is available for download at http://www.tbi.univie.ac.at/RNA.

Abstract

Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely used as a basis to explain experimental findings. Based on carefully measured thermodynamic parameters, exact dynamic programming algorithms can be used to compute ground states, base pairing probabilities, as well as thermodynamic properties. The ViennaRNA Package has been a widely used compilation of RNA secondary structure related computer programs for nearly two decades. Major changes in the structure of the standard energy model, the Turner 2004 parameters, the pervasive use of multi-core CPUs, and an increasing number of algorithmic variants prompted a major technical overhaul of both the underlying RNAlib and the interactive user programs. New features include an expanded repertoire of tools to assess RNA-RNA interactions and restricted ensembles of structures, additional output information such as centroid structures and maximum expected accuracy structures derived from base pairing probabilities, or z-scores for locally stable secondary structures, and support for input in fasta format. Updates were implemented without compromising the computational efficiency of the core algorithms and ensuring compatibility with earlier versions. The ViennaRNA Package 2.0, supporting concurrent computations via OpenMP, can be downloaded from http://www.tbi.univie.ac.at/RNA .