• 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...
  • 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...
  • 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...
  • 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...
  • 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...
  • RSEARCH

  • Referenced in 10 articles [sw23815]
  • homologs of single structured RNA sequences. BACKGROUND: For many RNA molecules, secondary structure rather than ... 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 ... pair and single nucleotide substitution matrices for RNA sequences called RIBOSUM matrices. RSEARCH reports...
  • Lynx

  • Referenced in 9 articles [sw13643]
  • study from computational biology, namely, the RNA secondary structure prediction problem. The constraints that make...
  • GenRGenS

  • Referenced in 7 articles [sw09070]
  • generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also...
  • 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 ... specific platform. In order for structure prediction researchers to better understand the results of their ... multiplatform visualization tool capable of displaying RNA secondary structures encoded in a variety of file...
  • 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...
  • PseudoViewer3

  • Referenced in 6 articles [sw17134]
  • user to ensure that the structure graph is overlap-free. Many programs such ... almost only program that automatically draws RNA secondary structures with pseudoknots. The previous version ... PseudoViewer visualizes all the known types of RNA pseudoknots as planar drawings, but visualizes some...
  • 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...
  • RNAstructure

  • Referenced in 3 articles [sw17133]
  • RNAstructure: software for RNA secondary structure prediction and analysis. Background: To understand an RNA sequence ... interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used ... structure of an RNA sequence. Results: RNAstructure is a software package for RNA secondary structure ... extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package...
  • Infernal

  • Referenced in 11 articles [sw17000]
  • profiles of the sequence and secondary structure of an RNA family called covariance models...
  • 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...
  • 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...
  • TPstructure

  • Referenced in 3 articles [sw23814]
  • 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 ... extension of the grammar for secondary structures and employs an enhancement by labelings ... context-free grammar for pk-structures, using data of RNA sequences and structures. The induced...
  • RNACompress

  • Referenced in 2 articles [sw35325]
  • compression and informational complexity measurement of RNA secondary structure. Results: RNACompress employs an efficient grammar ... design a suitable model to represent RNA secondary structure as well as derive the informational ... universal algorithm for the compression of RNA secondary structure as well as the evaluation ... measurement of the informational complexity of RNA secondary structure, which can be used to study...
  • 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 ... used to study the characteristics of RNA secondary ... structures, RNA structure conformational switches, RNA conformational energy landscapes and RNA secondary structure prediction based...