• TPstructure

  • Referenced in 3 articles [sw23814]
  • grammar, RNAFeatures*, capable of generating any RNA structure including pseudoknot structures (pk-structure). We represent ... their topological genus. Within this framework, RNA secondary structures correspond to pk-structures of genus ... RNAFeatures* acts on formal, arc-labeled RNA secondary structures, called λ-structures. λ-structures correspond ... structures, using data of RNA sequences and structures. The induced grammar facilitates fast Boltzmann sampling...
  • VARNA

  • Referenced in 5 articles [sw16406]
  • Interactive drawing and editing of the RNA secondary structure. VARNA is a tool ... visualization and annotation of the secondary structure of RNA, designed as a companion software ... XFIG). It also allows manual modification and structural annotation of the resulting drawing using either...
  • 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 ... software. Detailed output, in the form of structure plots with or without reliability information, single...
  • RNA FRABASE

  • Referenced in 2 articles [sw20771]
  • three-dimensional fragments within RNA structures. The RNA FRABASE is a web-accessible engine with ... fragments within a set of RNA structures. This is a new tool to search ... analyse RNA structures, directed at the 3D structure modelling. The user needs to input either ... protein data bank (PDB)-deposited RNA structures and their complexes, (ii) a collection of atom...
  • R2R

  • Referenced in 2 articles [sw17140]
  • consensus features of these molecules. RNA structural diagrams are typically made either with general-purpose ... Since the inference of a consensus RNA structure typically requires a multiple-sequence alignment ... secondary structure models for novel RNA structures or to revise models when new representatives ... structural models of many diverse RNA structures with a more practical amount of effort...
  • PETcofold

  • Referenced in 3 articles [sw17127]
  • predicting conserved interactions and structures of two multiple alignments of RNA sequences. Motivation: Predicting ... methods have already been useful in RNA structure determination, we assume that conserved ... predict interactions and secondary structures of two multiple alignments of RNA sequences. Results: PETcofold ... evaluation of both RNARNA interaction and structure prediction, we were able to extract only...
  • HotKnots

  • Referenced in 4 articles [sw17267]
  • HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. We present HotKnots, a new heuristic ... algorithm for the prediction of RNA secondary structures including pseudoknots. Based on the simple idea...
  • DIAL

  • Referenced in 6 articles [sw13837]
  • pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing ... programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing ... alignment algorithm may be used to detect structurally similar occurrences of a user-specified ... most interest in attempts to identify RNA motifs. DIAL is available at http://bioinformatics.bc.edu/clotelab/DIAL....
  • RNACluster

  • Referenced in 2 articles [sw23124]
  • measure the (dis)similarity of RNA secondary structures including base pair distance, mountain distance, morphological ... string edit distance and our in-house structure matrix distance, and one effective cluster approach ... study the characteristics of RNA secondary structures, RNA structure conformational switches, RNA conformational energy landscapes ... RNA secondary structure prediction based on the clustering of structure ensemble...
  • NUCPLOT

  • Referenced in 4 articles [sw16870]
  • facilitates comparison of binding found in different structures. NUCPLOT is a completely automatic program, which ... will also work for certain protein-RNA structures...
  • RNACompress

  • Referenced in 2 articles [sw35325]
  • compression and informational complexity measurement of RNA secondary structure. Results: RNACompress employs an efficient grammar ... robust and effective way for RNA structural data compression; (2) design a suitable model ... represent RNA secondary structure as well as derive the informational complexity of the structural data ... universal algorithm for the compression of RNA secondary structure as well as the evaluation...
  • IPknot

  • Referenced in 3 articles [sw17124]
  • IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Motivation ... Pseudoknots found in secondary structures of a number of functional RNAs play various roles ... biological processes. Recent methods for predicting RNA secondary structures cover certain classes of pseudoknotted structures ... novel computational method for predicting RNA secondary structures with pseudoknots based on maximizing expected accuracy...
  • FRASS

  • Referenced in 2 articles [sw15707]
  • FRASS: the web-server for RNA structural comparison. Background: The impressive increase of novel ... RNA structures, during the past few years, demands automated methods for structure comparison. While many ... integrals and allows one to compare structures of RNA chains and to find similar entries ... reproduce satisfactorily the DARTS classification of RNA 3D structures and the classification of the SCOR...
  • 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 ... datasets showed a substantial improvement in RNA structure prediction by RNAG over extant prediction methods ... analysis of 17 RNA families showed that the RNAG sampled structures were generally compact around...
  • FR3D

  • Referenced in 5 articles [sw13838]
  • toward the end of the RNA 3D structure course materials at this link. WebFR3D ... under stable URLs. FR3D annotations of all RNA-containing PDB files are available by from ... structure of interest. You may also be interested in the RNA Basepair Catalog hosted...
  • 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 ... classical alignment (using only primary structure data) then improve it with the new algorithm ... been used to align RNA sequences of eubacterial large ribosomal subunit...
  • RNAmute

  • Referenced in 2 articles [sw17059]
  • mutational analysis of RNA secondary structures. RNA mutational analysis at the secondary-structure level ... structure based and relies on RNA secondary-structure prediction has been developed for assisting...
  • 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 ... provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks ... insight into the relative performance of RNA secondary structure prediction methods on RNAs of different...
  • 3DNA

  • Referenced in 3 articles [sw21991]
  • motifs found in both DNA and RNA structures. The analysis routines identify and categorize...
  • tRNAscan-SE

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