The ViennaRNA Package is a set of standalone programs and libraries used for prediction and analysis of RNA secondary structures. The source code for the package is distributed freely and compiled binaries are available for

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which ...

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and

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platforms. The original paper has been cited over 2000 times.

Background

The three dimensional structure of biological macromolecules like

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

s and

nucleic acid Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main cl ...

s play critical role in determining their functional role. This process of decoding function from the sequence is an experimentally and computationally challenging question addressed widely.

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

structures form complex secondary and

tertiary structures Biomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length sc ...

compared to DNA which form

duplexes A duplex house plan has two living units attached to each other, either next to each other as townhouses, condominiums or above each other like apartments. By contrast, a building comprising two attached units on two distinct properties is ...

with full complementarity between two strands. This is partially because the extra oxygen in RNA increases the propensity for hydrogen bonding in the nucleic acid backbone. The

base pairing A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

and base stacking interactions of RNA play critical role in formation of

ribosome Ribosomes ( ) are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation). Ribosomes link amino acids together in the order specified by the codons of messenger RNA (mRNA) molecules to ...

spliceosome A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs (snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to specifi ...

, or

tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino ac ...

Secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

prediction is commonly done using approaches like dynamic programming, energy minimisation (for most stable structure) and generating suboptimal structures. A large number of structure prediction tools have been implemented as well.

Development

The first version of the ViennaRNA Package was published by Hofacker et al. in 1994. The package distributed tools to compute either minimum free energy structures or partition functions of RNA molecules; both using the idea of

dynamic programming Dynamic programming is both a mathematical optimization method and a computer programming method. The method was developed by Richard Bellman in the 1950s and has found applications in numerous fields, from aerospace engineering to economics. I ...

. Non-thermodynamic criterion like formation of maximum matching or various versions of kinetic folding along with an inverse folding heuristic to determine structurally neutral sequences were implemented. Additionally, the package also contained a statistics suite with routines for

cluster analysis Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense) to each other than to those in other groups (clusters). It is a main task of ...

, statistical geometry, and split decomposition. The package was made available as library and a set of standalone routines.

Version 2.0

A number of major systemic changes were introduced in this version with the use of a new parametrized energy model (''Turner 2004''), restructuring of the RNAlib to support concurrent computations in thread-safe manner, improvements to the

API An application programming interface (API) is a way for two or more computer programs to communicate with each other. It is a type of software Interface (computing), interface, offering a service to other pieces of software. A document or standa ...

, and inclusion of several new auxiliary tools. For example, tools to assess RNA-RNA interactions and restricted ensembles of structures. Furthermore, other features included 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 FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program ...

format. The updates, however, are compatible with earlier versions without affecting the computational efficiency of the core algorithms.

Web server

The tools provided by the ViennaRNA Package are also available for public use through a web interface.

Tools

In addition to prediction and analysis tools, the ViennaRNA Package contains several scripts and utilities for plotting and input-output processing. A summary of the available programs is collected in the table below (an exhaustive list with examples can be found in the official documentation).

References