• CompaRNA

  • Referenced in 2 articles [sw16474]
  • continuous benchmarking of automated methods for RNA secondary structure prediction. We present a continuous benchmarking ... approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA ... comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank ... insight into the relative performance of RNA secondary structure prediction methods on RNAs of different...
  • RNAmute

  • Referenced in 2 articles [sw17059]
  • server for the mutational analysis of RNA secondary structures. RNA mutational analysis at the secondary ... evolution occurs, and mutational analysis relating to structure should gain a better understanding of system ... structure based and relies on RNA secondary-structure prediction has been developed for assisting...
  • RNAG

  • Referenced in 2 articles [sw17129]
  • Gibbs sampler for predicting RNA secondary structure for unaligned sequences. Motivation: RNA secondary structure plays ... interest in the prediction of secondary structures for RNA families. In this article, we present ... alignment algorithm, RNAG, to predict consensus secondary structures for unaligned sequences. It uses a blocked ... conditional probability distributions P(Structure | Alignment) and P(Alignment | Structure). Not surprisingly, there is considerable...
  • CENTROIDFOLD

  • Referenced in 2 articles [sw17123]
  • CENTROIDFOLD: a web server for RNA secondary structure prediction. The CentroidFold web server (http://www.ncrna.org/centroidfold/) is a web application for RNA secondary structure prediction powered ... data: a single RNA sequence and a multiple alignment of RNA sequences. It responses with ... secondary structure. Usage of the server is quite simple. You can paste a single RNA...
  • Mfold

  • Referenced in 41 articles [sw12672]
  • prediction of the secondary structure of single stranded nucleic acids. The objective of this ... server is to provide easy access to RNA and DNA folding and hybridization software...
  • ProbKnot

  • Referenced in 2 articles [sw17268]
  • ProbKnot: Fast prediction of RNA secondary structure including pseudoknots. It is a significant challenge ... predict RNA secondary structures including pseudoknots. Here, a new algorithm capable of predicting pseudoknots ... reported. ProbKnot assembles maximum expected accuracy structures from computed base-pairing probabilities ... comparing predicted structures with known structures for a large database of RNA sequences with fewer...
  • tRNAscan-SE

  • Referenced in 16 articles [sw08005]
  • practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based...
  • RnaViz

  • Referenced in 2 articles [sw35745]
  • RnaViz 2: an improved representation of RNA secondary structure. Summary: RnaViz has been developed ... create nice, publication quality drawings of RNA secondary structure. RnaViz 2 supports CT, DCSE...
  • MODENA

  • Referenced in 5 articles [sw23804]
  • functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since ... noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally...
  • Locomotif

  • Referenced in 3 articles [sw35380]
  • incorporating the established thermodynamic model of RNA secondary structure formation. (2) motifs are described graphically ... editor allows us to draw secondary structures, annotated with size and sequence information. They closely ... established, but informal way in which RNA motifs are communicated in the literature. Thus...
  • R-CHIE

  • Referenced in 1 article [sw17137]
  • server and R package for visualizing RNA secondary structures. Visually examining RNA structures can greatly ... secondary structure of the RNA, various methods have been devised for visualizing RNA secondary structures ... these methods depict a given RNA secondary structure as a planar graph consisting of base ... present an alternative method of depicting RNA secondary structure as arc diagrams. This is well...
  • RNAsubopt

  • Referenced in 6 articles [sw10506]
  • RNAsubopt 2.1.8: calculate suboptimal secondary structures of RNAs. reads RNA sequences from stdin ... default −e mode) calculates all suboptimal secondary structures within a user defined energy range above...
  • RNAexinv

  • Referenced in 2 articles [sw17114]
  • physical attributes. It is an extended inverse RNA folding program with the rationale behind that ... robustness. RNAexinv considers not only the secondary structure in order to design sequences, but also ... fully conform with the given RNA secondary structure, but they will strictly conform with ... RNA shape of the given secondary structure and thereby take into consideration the recommended values...
  • TurboFold

  • Referenced in 3 articles [sw17269]
  • TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. Conclusions: TurboFold ... iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately...
  • rna-state-inf

  • Referenced in 1 article [sw33162]
  • Improving RNA secondary structure prediction via state inference with deep recurrent neural networks. The problem ... generate auxiliary information for data-directed RNA secondary structure prediction. Typical tools for state inference ... paper presents a practical approach to RNA secondary structure inference centered around a deep learning ... data that can be incorporated into RNA secondary structure prediction via the Nearest Neighbor Thermodynamic...
  • R2R

  • Referenced in 2 articles [sw17140]
  • speed the depiction of aesthetic consensus RNA secondary structures. Background: With continuing identification of novel ... showing the consensus features of these molecules. RNA structural diagrams are typically made either with ... Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment ... create consensus sequence and secondary structure models for novel RNA structures or to revise models...
  • RNAlign

  • Referenced in 7 articles [sw33856]
  • Program: Alignment of RNA Sequences Using Both Primary and Secondary Structures. We have developed ... bank of aligned homologous RNA sequences. Given a common folding structure for the bank ... optimal both in terms of primary and secondary structure. This method is useful to align ... distinguished from domains with more variable secondary structure. An optimal alignment of a sequence...
  • RNAspa

  • Referenced in 2 articles [sw17131]
  • secondary structure of ncRNA molecules. Background: In recent years, RNA molecules that are not translated ... regarding ncRNA is to predict the secondary structure of a molecule from its sequence ... RNAspa program, which comparatively predicts the secondary structure for a set of ncRNA molecules ... molecule. We also show that RNA secondary structures can be compared very rapidly...
  • Densityfold

  • Referenced in 1 article [sw12673]
  • RNA secondary structure prediction via energy density minimization. There is a resurgence of interest ... RNA secondary structure prediction problem (a.k.a. the RNA folding problem) due to the discovery ... majority of the computational tools for RNA secondary structure prediction are based on free energy ... which aims to predict the secondary structure of an RNA sequence by minimizing...
  • LocARNAscan

  • Referenced in 2 articles [sw23118]
  • secondary structure alone informative for homology search and the detection of novel members of RNA ... into the correct secondary structure helpful for this task? RESULTS: Sequence-structure alignment ... local structures of the target sequence. CONCLUSIONS: Although we demonstrate that a purely structure-based ... from high throughput methods to determine RNA secondary structure. In transcriptome-wide applications, such methods...