A folding algorithm for extended RNA secondary structures

Siederdissen, Christian Höner zu; Bernhart, Stephan H.; Stadler, Peter F.; Hofacker, Ivo L.

doi:10.1093/bioinformatics/btr220

Cited by 62 publications

(42 citation statements)

References 31 publications

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“…The user can choose from five different types of shape resolution corresponding to different abstraction levels.Local installationNo(4)RNAsuboptCalculates all suboptimal secondary structures within a user-defined energy range above the MFE.Local installationNo(3)RNAwolfPredicts an extended structure (including non-canonical base pairs and structures composed of two-diagrams). The allowed base pairs can contain all 4 × 4 nt, and the nucleotide bonds are explicitly annotated with the paired edges and isostericity information.Local installationNo(40)SfoldStatistical sampling of all possible structures. The sampling is weighted by partition function probabilities.Local installationNo(6)UNAFoldAn integrated collection of programs that simulate folding, hybridization and melting pathways for one or two single-stranded nucleic acid sequences.…”

Section: Methodsmentioning

confidence: 99%

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Puton

Kozłowski

Rother

et al. 2013

Nucleic Acids Research

107

118

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We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks.

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Section: Methodsmentioning

confidence: 99%

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Puton

Kozłowski

Rother

et al. 2013

Nucleic Acids Research

107

118

View full text Add to dashboard Cite

show abstract

“…The CONTRAfold algorithm by Do et al 65 considers all 16 possible base pairings instead of just the canonical six. Another solution is to use the space of extended secondary structures, 66 which also considers all 16 possible base pairs and, in addition, explicitly annotates nucleotide pairings with the nucleotide edge engaged in pairing. As both of these models have basically no constraints, the space of candidate sequences is unrestricted.…”

Section: Computational Design Of Rnas With Complex Energy Landscapesmentioning

confidence: 99%

Computational design of RNAs with complex energy landscapes

et al. 2013

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RNA has become an integral building material in synthetic biology. Dominated by their secondary structures, which can be computed efficiently, RNA molecules are amenable not only to in vitro and in vivo selection, but also to rational, computation-based design. While the inverse folding problem of constructing an RNA sequence with a prescribed ground-state structure has received considerable attention for nearly two decades, there have been few efforts to design RNAs that can switch between distinct prescribed conformations. We introduce a user-friendly tool for designing RNA sequences that fold into multiple target structures. The underlying algorithm makes use of a combination of graph coloring and heuristic local optimization to find sequences whose energy landscapes are dominated by the prescribed conformations. A flexible interface allows the specification of a wide range of design goals. We demonstrate that bi- and tri-stable "switches" can be designed easily with moderate computational effort for the vast majority of compatible combinations of desired target structures. RNAdesign is freely available under the GPL-v3 license.

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“…Codon adaptation index (CAI) is belongs to the earliest ones [9]. Also, there are many software tools evaluating the amount of secondary structures in mRNA [10][11][12].…”

Section: Introductionmentioning

confidence: 99%

A web application for automatic prediction of gene translation elongation efficiency

Sokolov

Zuraev

Lashin

et al. 2015

Journal of Integrative Bioinformatics

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SummaryExpression efficiency is one of the major characteristics describing genes in various modern investigations. Expression efficiency of genes is regulated at various stages: transcription, translation, posttranslational protein modification and others. In this study, a special EloE (Elongation Efficiency) web application is described. The EloE sorts the organism's genes in a descend order on their theoretical rate of the elongation stage of translation based on the analysis of their nucleotide sequences. Obtained theoretical data have a significant correlation with available experimental data of gene expression in various organisms. In addition, the program identifies preferential codons in organism's genes and defines distribution of potential secondary structures energy in 5´ and 3´ regions of mRNA. The EloE can be useful in preliminary estimation of translation elongation efficiency for genes for which experimental data are not available yet. Some results can be used, for instance, in other programs modeling artificial genetic structures in genetically engineered experiments. The EloE web application is available at http://www-bionet.sscc.ru:7780/EloE.

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A folding algorithm for extended RNA secondary structures

Cited by 62 publications

References 31 publications

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

Computational design of RNAs with complex energy landscapes

A web application for automatic prediction of gene translation elongation efficiency

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