ViennaRNA Package 2.0

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 webcite.A typical single stranded-nucleic acid molecule has the propensity to form double helical structures causing the molecule to fold back onto itself. Simple rules of complementary base pairing govern this process, which results in a regular pattern of Watson-Crick and GU pairings (helices) and intervening stretches of less regularly ordered nucleotides (loops), collectively known as the molecule's secondary structure. Secondary structure elements may be placed in close spatial proximity allowing additional non-covalent interactions. These are not as frequent and often are energetically less favorable compared to canonical base pairs, thus rendering the 3-dimensional tertiary structure of an RNA to be dominated by the underlying scaffold of the secondary structure. The canonical base pairing governs not only the thermodynamics but also the folding kinetics, which can be approximated as a hierarchical process in which secondary structure i