The ViennaRNA Package is
software
Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications.
The history of software is closely tied to the development of digital comput ...
, a set of standalone programs and
libraries
A library is a collection of Book, books, and possibly other Document, materials and Media (communication), media, that is accessible for use by its members and members of allied institutions. Libraries provide physical (hard copies) or electron ...
used for predicting and analysing
RNA
Ribonucleic acid (RNA) is a polymeric molecule that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
nucleic acid secondary structure
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule.
The secondary structures of bi ...
s.
The
source code
In computing, source code, or simply code or source, is a plain text computer program written in a programming language. A programmer writes the human readable source code to control the behavior of a computer.
Since a computer, at base, only ...
for the package is released as
free and open-source software
Free and open-source software (FOSS) is software available under a license that grants users the right to use, modify, and distribute the software modified or not to everyone free of charge. FOSS is an inclusive umbrella term encompassing free ...
and compiled binaries are available for the
operating system
An operating system (OS) is system software that manages computer hardware and software resources, and provides common daemon (computing), services for computer programs.
Time-sharing operating systems scheduler (computing), schedule tasks for ...
s
Linux
Linux ( ) is a family of open source Unix-like operating systems based on the Linux kernel, an kernel (operating system), operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically package manager, pac ...
,
macOS
macOS, previously OS X and originally Mac OS X, is a Unix, Unix-based operating system developed and marketed by Apple Inc., Apple since 2001. It is the current operating system for Apple's Mac (computer), Mac computers. With ...
, and
Windows
Windows is a Product lining, product line of Proprietary software, proprietary graphical user interface, graphical operating systems developed and marketed by Microsoft. It is grouped into families and subfamilies that cater to particular sec ...
. The original paper has been cited over 2,000 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 residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
s and
nucleic acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nuclei ...
s play a 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 that is essential for most biological functions, either by performing the function itself (non-coding RNA) or by forming a template for the production of proteins (messenger RNA). RNA and deoxyrib ...
structures form complex secondary and
tertiary structures compared to
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
which form
duplexes
A duplex house plan has two living units attached to each other, either next to each other as townhouses, condominiums or one above the other like apartments. By contrast, a building comprising two attached units on two distinct properties is ...
with full
complementarity between two strands. This is partly 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 molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order s ...
,
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 sp ...
, or
tRNA
Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes). In a cell, it provides the physical link between the gene ...
.
Secondary structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. 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. Many
structure prediction tools have been implemented also.
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. 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 data analyzing technique in which task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more Similarity measure, similar (in some specific sense defined by the ...
, 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 application programming interface (
API
An application programming interface (API) is a connection between computers or between computer programs. It is a type of software interface, offering a service to other pieces of software. A document or standard that describes how to build ...
), and inclusion of several new auxiliary tools. For example, tools to assess RNA-RNA interactions and restricted ensembles of structures. Further, 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
See also
*
Nucleic acid structure determination
Experimental approaches of determining the Biomolecular structure, structure of nucleic acids, such as RNA and DNA, can be largely classified into biophysics, biophysical and biochemistry, biochemical methods. Biophysical methods use the fundamen ...
*
Nucleic acid structure prediction
Nucleic acid structure prediction is a computational method to determine ''secondary'' and ''tertiary'' nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure ...
*
List of RNA structure prediction software
This list of RNA structure prediction software is a compilation of software tools and web portals used for RNA structure prediction.
Single sequence secondary structure prediction.
Single sequence tertiary structure prediction
Comparative met ...
External links
*
*{{GitHub, ViennaRNA
Bioinformatics software
Bioinformatics algorithms
Computational biology