• Rfam

  • Referenced in 32 articles [sw04637]
  • collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance ... three broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing ... conserved secondary structure which may be better preserved than the RNA sequence. The CMs used ... Pfam. CMs can simultaneously model RNA sequence and the structure in an elegant and accurate...
  • ViennaRNA

  • Referenced in 20 articles [sw10504]
  • prediction and comparison of RNA secondary structures. RNA secondary structure prediction through energy minimization...
  • Pfold

  • Referenced in 12 articles [sw23813]
  • Knudsen, B.; Hein, J. J.: Pfold: RNA secondary structure prediction using stochastic context-free grammars ... RNA secondary structures are important in many biological processes and efficient structure prediction can give ... experimental investigations. Many available programs for RNA secondary structure prediction only use a single sequence ... presents a practical way of predicting RNA secondary structure that is especially useful when related...
  • RSEARCH

  • Referenced in 10 articles [sw23815]
  • RSEARCH: finding homologs of single structured RNA sequences. BACKGROUND: For many RNA molecules, secondary structure ... single RNA molecule on the basis of secondary structure. RESULTS: We have developed a program ... that takes a single RNA sequence with its secondary structure and utilizes a local alignment ... sequence programs in finding homologs of structured RNA sequences...
  • PseudoViewer3

  • Referenced in 6 articles [sw17134]
  • generating planar drawings of large-scale RNA structures with pseudoknots. Motivation: Pseudoknots in RNA structures ... make visualization of RNA structures difficult. Even if a pseudoknot itself is represented without ... crossing, visualization of the entire RNA structure with a pseudoknot often results in a drawing ... PseudoViewer for efficiently visualizing large RNA structures with any types of pseudoknots, both known...
  • CONTRAfold

  • Referenced in 8 articles [sw17117]
  • dominant strategy for single sequence RNA secondary structure prediction. More recently, stochastic context-free grammars ... alternative probabilistic methodology for modeling RNA structure. Unlike physics-based methods, which rely on thousands ... based models. CONTRAfold is a novel secondary structure prediction method based on conditional log-linear ... empirical measurement of thermodynamic parameters for RNA secondary structure prediction...
  • RNAsoft

  • Referenced in 7 articles [sw09073]
  • RNAsoft: a suite of RNA secondary structure prediction and design software tools ... predicting the secondary structure of a pair of DNA or RNA molecules, testing that combinatorial ... molecules have no unwanted secondary structure and designing RNA strands that fold to a given ... based on standard thermodynamic models of RNA secondary structure formation. RNAsoft can be found online...
  • Sfold

  • Referenced in 12 articles [sw23820]
  • sampling paradigm for the prediction of RNA secondary structure. One of the main objectives ... computational tools for the rational design of RNA-targeting nucleic acids, which include small interfering ... RNA folding algorithm to account for the likely existence of a population of structures...
  • SARSA

  • Referenced in 4 articles [sw13834]
  • used to align two or more RNA tertiary structures. The basic idea behind SARSA ... nucleotide conformations, via which we transform RNA 3D structures into 1D sequences of SA letters ... similarities. In SARSA, we provide two RNA structural alignment tools, PARTS for pairwise alignment ... RNA tertiary structures and MARTS for multiple alignment of RNA tertiary structures. Particularly in PARTS...
  • Infernal

  • Referenced in 11 articles [sw17000]
  • sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated ... Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden...
  • 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 ... exploring the RNA sequences folding into a user-given target structure. In the present study ... successfully design 23 RNA sequences folding into the target structures; this result is better than...
  • RNAforester

  • Referenced in 7 articles [sw15709]
  • experience with its use for RNA structure alignment. One enhancement is the introduction...
  • iPARTS

  • Referenced in 4 articles [sw13839]
  • improved tool of pairwise alignment of RNA tertiary structures. PARTS is an improved web server ... aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular ... finally use this SA to transform RNA 3D structures into 1D sequences of SA letters ... similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs...
  • ARTS

  • Referenced in 6 articles [sw13836]
  • ARTS: alignment of RNA tertiary structures, ARTS is a fully automated method for aligning ... DARTS classification database of all solved RNA 3D structures...
  • jViz.Rna

  • Referenced in 4 articles [sw17135]
  • JViz.Rna —a Java tool for RNA secondary structure visualization. Many tools have been developed ... visualization of RNA secondary structures using a variety of techniques and output formats. However, each ... enable life science researchers to interpret RNA structure easily, it is helpful to provide them ... multiplatform visualization tool capable of displaying RNA secondary structures encoded in a variety of file...
  • iSS-PseDNC

  • Referenced in 16 articles [sw22438]
  • important roles in gene structure annotation and even in RNA splicing. Although a series ... most of them neglected the intrinsic local structural properties. In the present study, a predictor ... sites and that the six DNA local structural properties described in this paper may provide ... depth investigations into the mechanism of RNA splicing...
  • Lynx

  • Referenced in 10 articles [sw13643]
  • study from computational biology, namely, the RNA secondary structure prediction problem. The constraints that make...
  • RNAstructure

  • Referenced in 3 articles [sw17133]
  • RNAstructure: software for RNA secondary structure prediction and analysis. Background: To understand an RNA sequence ... structure must be known. Furthermore, target RNA structure is an important consideration in the design ... interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used ... RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics...
  • RNAKinetics

  • Referenced in 4 articles [sw23818]
  • server that models secondary structure kinetics of an elongating RNA. The RNAKinetics server ... software models the dynamics of RNA secondary structure by the means of kinetic analysis ... kinetic ensemble, i.e. a collection of RNA structures that are endowed with probabilities, which depend ... RNA folding pathways, revealing important kinetic details that are not captured by the traditional structure...
  • GenRGenS

  • Referenced in 7 articles [sw09070]
  • generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also...