Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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Info and source of our software

And the god of application said "There should be no algorithm without available implementation!" and he was looking at us and saw it is all there!

Available software is divided into services that can be used directly with your browser and stuff that needs to be downloaded and most probably compiled to use it. If you're still reading this, you most likely are not afraid of compiling your own software, and may be glad to know, that most of our software available as webservices can also be downloaded and used as a standalone.

Webservices (may also be downloaded in some cases)

Downloadable Software

The software developed in our group is listed below in alphabetical order. However since the most prominent and thought after one is the Vienna RNA Package it is listed out of order at the top of the list.

Vienna RNA package

The Vienna RNA Package consists of a C-library and a set of stand-alone programs to solve problems related to RNA secondary structures. Among them are (sub)optimal structure prediction, RNA-RNA interaction analysis, energy evaluation, folding path identification, consensus structure prediction, and structural alignment.

Links

Publications

Fast Folding and Comparison of RNA Secondary Structures
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
In: Monatshefte Chemie, 1994, 125, 167-188
doi:10.1007/BF00818163 bibtex
ViennaRNA Package 2.0
Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
In: Algorithms Mol Biol., 2011, 6, 26
doi:10.1186/1748-7188-6-26 bibtex

alidot - Detecting Conserved RNA Structures

alidot is designed to detect conserved RNA secondary structures in small data sets of related RNA sequences. The method is a combination of structure prediction and comparative sequence alignment.

More information is contained in the README file. The program alidot and the associated perl scripts are part of the Vienna RNA Package.

Links

Publications

Automatic Detection of Conserved RNA Structure Elements in Complete RNA Virus Genomes
Ivo L. Hofacker, Martin Fekete, Christoph Flamm, Martijn A. Huynen, Susanne Rauscher, Paul E. Stolorz, Peter F. Stadler
In Nucl.Acids Res., 1998, 26, 3825-3836
doi:10.1093/nar/26.16.3825 bibtex
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes
Ivo L. Hofacker and Peter F. Stadler
In Comp Chem., 1999, 23, 401-414
doi:10.1016/S0097-8485(99)00013-3 bibtex

AREsite - database for the detailed investigation of AU-rich elements

AREsite is an online resource for the investigation of AU-rich elements (ARE) in vertebrate mRNA UTR sequences hosted at the Institute of Theoretical Chemistry, University of Vienna. AREs are one of the most prominent cis-acting regulatory elements found in 3' vertebrate, untranslated regions of mRNAs. Various ARE-binding proteins that possess RNA stabilizing or destabilizing functions are recruited by sequence-specific motifs. This online resource allows detailed investigation of these functional elements by analysis of the phylogentic conservation and the structural context these motifs are embedded in. Moreover, AREsite provides information about experimentally validated targets from extensive literature search.

Links

Publications

AREsite: a database for the comprehensive investigation of AU-rich elements
Andreas R Gruber, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, Ivo L Hofacker
In Nucleic Acids Research, 2011, 39, Database issue, D66-D69
doi:10.1093/nar/gkq990 bibtex

barriers - Basin Structure of RNA Energy Landscapes

barriers reads an energy sorted list of conformations of a landscape, and computes local minima and energy barriers of the landscape. For each local minimum found it prints the conformation of the minimum, its energy, the number of the "parent"-minimum it merges with, and the height of the energy barrier. Additional information on each minimum, such as saddle point conformation, basin sizes, etc. can be gathered as well.

The barriers program is fundamental to compute global folding kinetics (using treekin) of RNA molecules.

Links

Publications

Barrier Trees of Degenerate Landscapes
Christoph Flamm, Ivo L Hofacker, Peter F Stadler, Michael T Wolfinger
In Zeitschrift für Physikalische Chemie, 2002, 216, 2, 155
doi:10.1524/zpch.2002.216.2.155 bibtex
Efficient computation of RNA folding dynamics
Michael T Wolfinger, W Andreas Svrcek-Seiler, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
In Journal of Physics A: Mathematical and General, 2004, 37, 17, 4731-4741
doi:10.1088/0305-4470/37/17/005 bibtex

barMap

Links

Publications

BarMap: RNA folding on dynamic energy landscapes
Ivo L Hofacker, Christoph Flamm, Christian Heine, Michael T Wolfinger, Gerik Scheuermann, Peter F Stadler
In RNA, 2010, 16, 7, 1308-1316
doi:10.1261/rna.2093310 bibtex

Basin hopping graph framework

B(asin)H(opping)G(raph) is a novel coarse-grained model to approximate the folding landscapes of RNA molecules. Each vertex of the BHG is a local minimum, which represents the corresponding basin in the landscape. Its edges connect basins when there exists an ``energetically favorable'' direct transition between them. The weights on the edges are the corresponding saddle heights and thus measure the difficulties of these favorable transitions. BHGs can be approximated efficiently and with high accuracy for RNAs well beyond the length range accessible to enumerative algorithms. The BHG contains more information than the barrier tree. The barrier tree is equivalent to the dendrogram obtained from the BHG by single linkage clustering. Efficient heuristics are utilized to overcome the stringent length restrictions imposed by enumerative approaches. The framework consists of two largely independent components:

  1. The RNAlocmin program generates a sample set of local minima within a user-defined energy range above the ground state. This component replaces the exhaustive enumeration of all low energy states and uses an adaptive schedule for setting up its parameters.
  2. The BHGbuilder algorithm is then used to estimate direct saddle points and to determine BHG-adjacency on the input set of LMs. As we show below, the edges and edge weights can be estimated along the way.

Links

Bcheck - rnpB gene prediction

Bcheck is a wrapper tool for rnpB gene prediction by combining speed of rnabob descriptor model and sensitivity of infernal covariance model.

Links

Publications

Bcheck: a wrapper tool for detecting RNase P RNA genes
Dilmurat Yusuf, Manja Marz, Peter F Stadler, Ivo L Hofacker
In BMC Genomics, 2010, 11, 1, 432
doi:10.1186/1471-2164-11-432 bibtex

codaln - Alignments of Nucleic Acid Sequences

codaln produces multiple nucleic acid alignments using information on coding and non-coding regions as part of the scoring function. This is done in order to prevent the problem of higher sequence divergency on the level of nucleic acids as compared to the underlying protein sequences in the case of coding at a certain region of the input nucleic acid sequences.

Links

Publications

Multiple sequence alignments of partially coding nucleic acid sequences
Roman R Stocsits, Ivo L Hofacker, Claudia Fried, Peter F Stadler
BMC Bioinformatics, 2005, 6(1), 160
doi:10.1186/1471-2105-6-160 bibtex
Nucleic Acid Sequence Alignments of Partly Coding Regions
Roman R. Stocsits
Dissertation, 2003, University of Vienna

CMcompare

The CMCompare program takes two Infernal covariance models and calculates the Link sequence and its Link score. The Link sequence is the sequence scored by both models highest at the same time. Two models with a high Link score are not well separated from each other.

Links

Publications

Discriminatory power of RNA family models
Höner zu Siederdissen, Christian and Hofacker, Ivo L.
Bioinformatics, 2010, 26, 453-459
doi:10.1093/bioinformatics/btq370 bibtex

cycdeco - Relevant Cycles of undirected graphs

cycdeco reads undirected unweighted graphs (GML-format) and calculates a minimum cycle bases, the set of relevant cycles, the set of shortest and unique shortest and essential cycles, or the interchangeability classes of relevant cycles.

Links

Publications

A note On Minimum Path Bases
Petra M. Gleiss, Josef Leydold, Peter F. Stadler
Presented at the conference Recent Trends in Graph Theory, Algebraic Combinatorics, and Graph Algorithms, Bled (Slovenia) Sep 24-27 2001.
Abstract
Relevant Cycles in Chemical Reaction Network
Petra M. Gleiss, Peter F. Stadler, A. Wagner, and David A. Fell
In Adv. Complex Systems, 2001, 4, 207-226
Abstract bibtex

Graph Grammar Library (GGL)

A rule based chemical reaction application

Links

Publications

The Graph Grammar Library - a generic framework for chemical graph rewrite systems
Martin Mann, Heinz Ekker, and Christoph Flamm
In Proc. of International Conference on Model Transformation (ICMT) 2013, LNCS, Pages 52-53, (2013). ISBN: 978-3-642-38882-8 (Print) 978-3-642-38883-5 (Online)
doi:10.1007/978-3-642-38883-5_5
Evolution of metabolic networks: a computational framework
Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider, Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L Hofacker, Peter F Stadler
In Journal of Systems Chemistry, 2010, 1, 1, 1-14
doi:10.1186/1759-2208-1-4 bibtex
A graph-based toy model of chemistry
Gil Benkö, Christoph Flamm, Peter F Stadler
In Journal of Chemical Information and Computer Sciences, 2003, 43, 4, 1085-1093
doi:10.1021/ci0200570 bibtex

kinfold - Kinetic folding of RNA

The program Kinfold simulates the stochastic folding kinetics of RNA sequences into secondary structures. The algorithm operates on the basis of the formation, dissociation, and the shifting of individual base pairs. For the energy evaluation of RNA secondary structures Kinfold uses routines from the Vienna RNA Package and is also distributed with the package.

Links

Publications

RNA Folding at Elementary Step Resolution
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
In RNA, 2000, 6, 325-338
doi:10.1017/S1355838200992161 bibtex

probA - Stochastic pairwise sequence alignment

probA enables global pairwise alignment using the partition function over all canonical alignments to calculate the probability of every match between a position in the first and a position in the second sequence. For the calculation of the partition function we used a modified alignment algorithm that avoids the generation of solutions that are represented differently but are equivalent from a semantic point of view. Furthermore we include a parameter governing the relative weight of alignment paths with different scores (Kschischo 2000) and extend previous approaches to stochastic pairwise alignments by a stochastic backtracking procedure that can be used to obtain ensembles of suboptimal alignments with correct statistical weights.

Links

Publications

Stochastic pairwise alignments
Ulrike Mückstein, Ivo L. Hofacker, and Peter F. Stadler
In Bioinformatics, 2002, 18 Suppl 2, ii, S153-S160
doi:10.1093/bioinformatics/18.suppl_2.S153 bibtex

RNAwolf

The RNAwolf algorithm provides extended RNA secondary structure predictions. In extended secondary structures, each nucleotide can engage in a pairing with up two other nucleotides. Furthermore the paired edge (Watson-Crick, Sugar, Hoogsteen) for each nucleotide is predicted.

Links

Publications

A Folding Algorithm for Extended RNA Secondary Structures
Höner zu Siederdissen, Christian and Bernhart, Stephan H. and Stadler, Peter F. and Hofacker, Ivo L.
Bioinformatics, 2011, 27, 129-136
doi:10.1093/bioinformatics/btr220 bibtex

RNApredator - Prediction of bacterial sRNA targets

The RNApredator software facilitates the prediction of sRNA-mRNA interactions in bacteria. Currently targets can be searched in more than 1300 bacterial species. RNApredator uses a dynamic programming approach to compute putative targets. The main machinery used by RNApredator to find targets is the program called RNAplex. RNAplex is a new approach for RNA-RNA interaction search, which has a prediction accuracy similar to that of algorithms that explicitly consider intramolecular structures, but running at least three orders of magnitude faster than RNAup and IntaRNA. This is achieved by using a combination of pre-computed accessibility profiles, with an approximate energy- model, allowing to mimic the effects of the competition between intra- and intermolecular interactions.

Links

Publications

RNApredator: fast accessibility-based prediction of sRNA targets
Florian Eggenhofer, Hakim Tafer, Peter F Stadler, Ivo L Hofacker
In Nucleic Acids Research, 2011, 39, Web Server issue, W149-W154
doi:10.1093/nar/gkr467 bibtex

RNAstrand - Plus/Minus strand prediction of structured RNAs

The RNAstrand web server predicts the reading direction (plus or minus strand) of a structured RNA in a multiple sequence alignment.

Links

Publications

RNAstrand: Reading Direction of Structured RNAs in Multiple Sequence Alignments
Kristin Reiche and Peter F. Stadler,
In Algorithms for Molecular Biology, 2007, 2, 6
doi:10.1186/1748-7188-2-6 bibtex

RNAxs - siRNA design

RNAxs will help you to design potent siRNAs to knock down your gene(s) of interest. RNAxs is based on the RNAplfold program to assess the mRNA target site accessibility. RNAxs was trained on two different datasets, one targeting 3'UTRs and the other one designed to repress coding sequences only.

Links

Publications

The impact of target site accessibility on the design of effective siRNAs.
Hakim Tafer, Stefan L Ameres, Gregor Obernosterer, Christoph A Gebeshuber, Renée Schroeder, Javier Martinez, Ivo L Hofacker
In Nature Biotechnology, 2008, 26, 5, 578-583
10.1038/nbt1404 bibtex

RNAz - Non-coding RNA prediction

RNAz detects functional RNA secondary structures in multiple sequence alignment based on two characteristic features: (i) thermodynamic stability, (ii) structural conservation.

Links

Publications

Fast and reliable prediction of noncoding RNAs
Stefan Washietl, Ivo L. Hofacker, and Peter F. Stadler
In Proc. Natl. Acad. Sci. U.S.A., 2005, 102, 2454-2459
doi:10.1073/pnas.0409169102 bibtex
Secondary structure prediction for aligned RNA sequences
Hofacker IL, Fekete M, and Stadler PF
In Journal of Molecular Biology, 2002, 319, 1059-1066
doi:10.1016/S0022-2836(02)00308-X bibtex

SOSlib - The SBML ODE Solver Library

SOSlib is both a programming library and a command-line application for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML). The package employs libSBML's AST (Abstract Syntax Tree) for formula representation to construct ODE systems, their Jacobian matrix and other derivatives. CVODES, the sensitivity-enabled ODE solver in the SUNDIALS package is used for numerical integration and sensitivity analysis of stiff and non-stiff ODE systems.

Links

Publications

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks
Rainer Machné, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, Christoph Flamm
In Bioinformatics, 2006, 22, 11, 1406-1407
doi:10.1093/bioinformatics/btl086 bibtex

Structure Conservation Analysis

The Structure Conservation Analysis web server will help you to detect evolutionarily conserved RNA secondary structures in multiple sequence alignments.

Links

treekin - Folding dynamics via numerical integration

The program treekin computes folding dynamics based on a given rate matrix. Usually, it operates on coarse grained versions of an energy landscape, where all conformations belonging to the same local minimum have been contracted into a single macro-state. treekin reads in the a list of local minima (macro-states) and effective refolding rates between these minima as computed by barriers --rates. Since the the number of macro-states is small (typically on the order of 100—1000), folding dynamics can be computed by direct numerical integration of the master equation conformations (i.e. diagonalization of the rate matrix).

Links

Publications

Efficient computation of RNA folding dynamics
Michael T Wolfinger, W Andreas Svrcek-Seiler, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
In Journal of Physics A: Mathematical and General, 2004, 37, 17, 4731-4741
doi:10.1088/0305-4470/37/17/005 bibtex

Vienna Reaction Network Library (Vienna-RNL)

The Vienna Reaction Network Library Vienna-RNL implements basic set-theoretic operations on chemical reaction networks. It provides basic ANSI C data structures for chemical reactions and their networks, operations such as the union, intersection, or difference of chemical reaction networks.

Links