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171
Sfold web server for statistical folding and rational design of nucleic acids
- Nucleic Acids Res
, 2004
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Partition function and base pairing probabilities of RNA heterodimers
- Algorithms Mol Biol
, 2006
"... Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inte ..."
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Cited by 65 (14 self)
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Abstract Background: RNA has been recognized as a key player in cellular regulation in recent years. In many cases, noncoding RNAs exert their function by binding to other nucleic acids, as in the case of microRNAs and snoRNAs. The specificity of these interactions derives from the stability of inter-molecular base pairing. The accurate computational treatment of RNA-RNA binding therefore lies at the heart of target prediction algorithms. Methods: The standard dynamic programming algorithms for computing secondary structures of linear singlestranded RNA molecules are extended to the co-folding of two interacting RNAs. Results: We present a program, RNAcofold, that computes the hybridization energy and base pairing pattern of a pair of interacting RNA molecules. In contrast to earlier approaches, complex internal structures in both RNAs are fully taken into account. RNAcofold supports the calculation of the minimum energy structure and of a complete set of suboptimal structures in an energy band above the ground state. Furthermore, it provides an extension of McCaskill's partition function algorithm to compute base pairing probabilities, realistic interaction energies, and equilibrium concentrations of duplex structures.
Abstract shapes of RNA
- Nucleic Acids Res
, 2004
"... The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, howeve ..."
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Cited by 65 (13 self)
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The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamentaldifferences,or, inotherwords, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of severalRNAs.For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.
Thermodynamics of RNA-RNA Binding
, 2005
"... Background: Reliable predictions of RNA-RNA binding energies is crucial e.g. for the understanding on RNAi, microRNA-mRNA binding, and antisense interactions. The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to “open ” ..."
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Cited by 63 (13 self)
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Background: Reliable predictions of RNA-RNA binding energies is crucial e.g. for the understanding on RNAi, microRNA-mRNA binding, and antisense interactions. The thermodynamics of such RNA-RNA interactions can be understood as the sum of two energy contributions: (1) the energy necessary to “open ” the binding site, and (2) the energy gained from hybridization. Methods: We present an extension of the standard partition function approach to RNA secondary structures that computes the probabilities Pu[i, j] that a sequence interval [i, j] is unpaired. Results: Comparison with experimental data shows that Pu[i, j] can be applied as a significant determinant of local target site accessibility for RNA interference (RNAi). Furthermore, these quantities can be used to rigorously determine binding free energies of short oligomers to large mRNA targets. The resource consumption is comparable to a single partition function computation for the large target molecule. We can show that RNAi efficiency correlates well with the binding energies of siRNAs to their respective mRNA target.
Thermodynamic analysis of interacting nucleic acid strands
- SIAM Rev
, 2007
"... Abstract. Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary stru ..."
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Cited by 52 (4 self)
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Abstract. Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and distinguishability issues that do not arise for single-stranded structures. We then derive the form of the partition function for a fixed volume containing a dilute solution of nucleic acid complexes. This expression can be evaluated explicitly for small numbers of strands, allowing the calculation of the equilibrium population distribution for each species of complex. Alternatively, for large systems (e.g., a test tube), we show that the unique complex concentrations corresponding to thermodynamic equilibrium can be obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality.
Predicting a set of minimal free energy RNA secondary structures common to two sequences
- Bioinformatics
, 2005
"... Function derives from structure; therefore there is need of methods for predicting functional RNA structures. Results: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low energy structu ..."
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Cited by 45 (6 self)
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Function derives from structure; therefore there is need of methods for predicting functional RNA structures. Results: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low energy structures. Dot plots can be drawn to show all base pairs in structures within an energy increment. Dynalign predicts more well-defined structures than structure prediction using a single sequence; in 5S rRNA sequences, the average number of base pairs in structures with energy within 20 % of the lowest energy structure is 317 using Dynalign, but 569 using a single sequence. Structure prediction with Dynalign can also be constrained according to experiment or comparative analysis. The accuracy, measured as sensitivity and positive predictive value, of Dynalign is greater than predictions with a single sequence. Availability: Dynalign can be downloaded at
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
- Bioinformatics
, 2007
"... Motivation: As more non–coding RNAs are discovered, the import-ance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is ..."
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Cited by 28 (2 self)
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Motivation: As more non–coding RNAs are discovered, the import-ance of methods for RNA analysis increases. Since the structure of ncRNA is intimately tied to the function of the molecule, programs for RNA structure prediction are necessary tools in this growing field of research. Furthermore, it is known that RNA structure is often evolutionarily more conserved than sequence. However, few exi-sting methods are capable of simultaneously considering multiple sequence alignment and structure prediction. Results: We present a novel solution to the problem of simulta-neous structure prediction and multiple alignment of RNA sequences. Using Markov chain Monte Carlo in a simulated annealing framework, the algorithm MASTR (Multiple Alignment of ST ructural RNAs) ite-ratively improves both sequence alignment and structure prediction for a set of RNA sequences. This is done by minimizing a combi-ned cost function that considers sequence conservation, covariation and basepairing probabilities. The results show that the method is very competitive to similar programs available today, both in terms of accuracy and computational efficiency.
Simulating RNA folding kinetics on approximated energy landscapes
- Journal of Molecular Biology
, 2008
"... of Molecular Biology (2008), doi: 10.1016/j.jmb.2008.02.007 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of th ..."
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Cited by 20 (2 self)
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of Molecular Biology (2008), doi: 10.1016/j.jmb.2008.02.007 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AC CE
