• Rfam

  • Referenced in 33 articles [sw04637]
  • represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). The families ... broad functional classes: non-coding RNA genes, structured cis-regulatory elements and self-splicing RNAs ... functional RNAs often have a conserved secondary structure which may be better preserved than...
  • Mfold

  • Referenced in 41 articles [sw12672]
  • prediction of the secondary structure of single stranded nucleic acids. The objective of this...
  • ViennaRNA

  • Referenced in 20 articles [sw10504]
  • prediction and comparison of RNA secondary structures. RNA secondary structure prediction through energy minimization ... range of the optimal energy. For secondary structure comparison, the package contains several measures...
  • Pfold

  • Referenced in 12 articles [sw23813]
  • Hein, J. J.: Pfold: RNA secondary structure prediction using stochastic context-free grammars. RNA secondary ... investigations. Many available programs for RNA secondary structure prediction only use a single sequence ... obtain related RNA sequences with conserved secondary structure. These should be included in structural analyses ... practical way of predicting RNA secondary structure that is especially useful when related sequences...
  • RSEARCH

  • Referenced in 10 articles [sw23815]
  • sequences. BACKGROUND: For many RNA molecules, secondary structure rather than primary sequence is the evolutionarily ... molecule on the basis of secondary structure. RESULTS: We have developed a program, RSEARCH, that ... single RNA sequence with its secondary structure and utilizes a local alignment algorithm to search...
  • tRNAscan-SE

  • Referenced in 16 articles [sw08005]
  • covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars...
  • Rnamotif

  • Referenced in 10 articles [sw04638]
  • sequences that match a ”motif” describing secondary structure interactions. A match means that the given ... capable of adopting the given secondary structure, but is not intended to be predictive. Matches...
  • iProt-Sub

  • Referenced in 14 articles [sw27604]
  • proteases). iProt-Sub integrates heterogeneous sequence and structural features and uses a two-step feature ... including local amino acid sequence profile, secondary structure, solvent accessibility and native disorder, which will...
  • PSIPRED

  • Referenced in 14 articles [sw11340]
  • protein structure prediction server. The PSIPRED protein structure prediction server allows users to submit ... their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version...
  • RNAsoft

  • Referenced in 7 articles [sw09073]
  • RNAsoft: a suite of RNA secondary structure prediction and design software tools ... programs provides tools for predicting the secondary structure of a pair ... molecules have no unwanted secondary structure and designing RNA strands that fold to a given ... input secondary structure. The tools are based on standard thermodynamic models of RNA secondary structure...
  • 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 ... measurement of thermodynamic parameters for RNA secondary structure prediction...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • defined in terms of secondary structure, solvent accessibility, and hydrogen bonding status. The environment-specific ... accessibility, its position relative to the secondary structure elements (SSEs) and the conservation...
  • Sfold

  • Referenced in 13 articles [sw23820]
  • paradigm for the prediction of RNA secondary structure. One of the main objectives of this...
  • JPred

  • Referenced in 7 articles [sw35977]
  • JPred: a consensus secondary structure prediction server. An interactive protein secondary structure prediction Internet server ... submitted, and returns predictions from six secondary structure prediction algorithms that exploit evolutionary information from...
  • RNAlign

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

  • Referenced in 8 articles [sw12671]
  • from “Unified Nucleic Acid Folding.” Folding (secondary structure) prediction for single-stranded ... including Mac OS X. Images of secondary structures, hybridizations, and dot plots may be computed...
  • Infernal

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

  • Referenced in 7 articles [sw23805]
  • predicting stability of nucleic acid secondary structure. The Nearest Neighbor Database (NNDB, http://rna.urmc.rochester.edu/NNDB) ... parameter sets for predicting nucleic acid secondary structure stabilities. For each set of parameters...
  • Lynx

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

  • Referenced in 18 articles [sw17207]
  • protein is then inferred by structurally matching the 3D models with other known proteins ... server run contains full-length secondary and tertiary structure predictions, and functional annotations on ligand...