• RNAMotifContrast

  • Referenced in 1 article [sw39987]
  • method to discover and visualize RNA structural motif subfamilies. Understanding the 3D structural properties ... analysis of RNA properties by recognizing structural motifs, they do not provide the means ... analyzing the similarities and variations of RNA structural motif characteristics. In this method, a graph ... RNAMotifContrast on a dataset of known RNA structural motif families. From the results, we observed...
  • Rnamotif

  • Referenced in 10 articles [sw04638]
  • database for RNA sequences that match a ”motif” describing secondary structure interactions. A match means...
  • RNAfbinv

  • Referenced in 1 article [sw17115]
  • interested in preserving a particular RNA secondary structure motif, or fragment, for biological reasons ... sequence, or both. Thus, the inverse RNA folding problem could benefit from considering fragment constraints ... this shape-based design approach, specific RNA structural motifs with known biological functions are strictly...
  • Rnall

  • Referenced in 1 article [sw23119]
  • motifs and study functions of RNA molecules. Most of the current RNA secondary structure prediction ... energy landscape for illustrating RNA LSS, which may facilitate RNA motif mining on the genomic ... well with known RNA motifs. CONCLUSIONS: Rnall is designed for RNA LSS prediction and together ... features that could be used for RNA structural motif mining. Rnall is freely available...
  • Rnabob

  • Referenced in 2 articles [sw04636]
  • program to search for RNA secondary structure motifs in sequence databases...
  • Locomotif

  • Referenced in 3 articles [sw35380]
  • previous ones in three ways: (1) motif search is based on efficient dynamic programming algorithms ... established thermodynamic model of RNA secondary structure formation. (2) motifs are described graphically, using ... 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...
  • RNASTAR

  • Referenced in 1 article [sw17132]
  • into evolutionary principles governing change in RNA structural motifs. The improved alignments have been contributed...
  • RNAstrand

  • Referenced in 1 article [sw23126]
  • putative ncRNA genes and other structured RNA motifs. A prerequisite for their functional annotation ... precision. RESULTS: While folding energies of an RNA and its reverse complement are similar ... conjunction with substitution patterns to discriminate between structured RNAs and their complements. We present here...
  • patteRNA

  • Referenced in 1 article [sw33164]
  • pattern recognition algorithm that rapidly mines RNA structure motifs from structure profiling data. It features...
  • 3DNA

  • Referenced in 4 articles [sw21991]
  • complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines identify...
  • VeRNAl

  • Referenced in 1 article [sw39988]
  • VeRNAl: Mining RNA Structures for Fuzzy Base Pairing Network Motifs. RNA 3D motifs are recurrent ... pair interactions, which are crucial for understanding structure-function relationships. The task of automatically identifying ... motifs is computationally hard, and remains a key challenge in the field of RNA structural ... problem by constraining the structural variability in occurrences of a motif, and narrowing the substructure...
  • RAG

  • Referenced in 1 article [sw21205]
  • approach for organizing RNA secondary structures, including existing and hypothetical motifs. Description: We now present ... classes of RNA secondary motifs, assists identification of structural and functional properties of user-supplied ... novel RNAs based on predicted candidate motifs...
  • RNABC

  • Referenced in 1 article [sw10929]
  • atom coordinate file for an RNA crystal structure (usually from the MolProbity web service), with ... RNABC, first on the S-motifs from 42 RNA structures, and second on the worst ... outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems...
  • CMfinder

  • Referenced in 6 articles [sw17265]
  • tool to predict RNA motifs in unaligned sequences. It is an expectation maximization algorithm using ... motif description, featuring novel integration of multiple techniques for effective search of motif space ... folding energy-based approaches to predict structure in a principled way. Extensive tests show that ... highly accurate covariance models of known RNA motifs based on small numbers of related sequences...
  • SARSA

  • Referenced in 4 articles [sw13834]
  • MARTS for multiple alignment of RNA tertiary structures. Particularly in PARTS, we have implemented four ... comparing whole structural similarity, (ii) semiglobal alignment for detecting structural motifs, (iii) local alignment ... tools in SARSA take as input RNA 3D structures in the PDB format...
  • DIAL

  • Referenced in 6 articles [sw13837]
  • programming algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing ... Smith–Waterman) and semiglobal (modified to yield motif search). Suboptimal alignments are optionally returned ... detect structurally similar occurrences of a user-specified 3D motif. The query motif ... semiglobal motif search may be of most interest in attempts to identify RNA motifs. DIAL...
  • iPARTS

  • Referenced in 4 articles [sw13839]
  • similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs ... determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments ... rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online...
  • MINT

  • Referenced in 1 article [sw16407]
  • motifs and short-range interactions in trajectories of nucleic acids. Structural biology experiments and structure ... structures on microsecond time scales. Therefore, we can generate the dynamics of DNA or RNA ... Motif Identifier for Nucleic acids Trajectory) — an automatic tool for analyzing three-dimensional structures ... base pairing patterns, identifies secondary structure motifs (helices, junctions, loops, etc.) and pseudoknots. MINT also...
  • ARTS

  • Referenced in 6 articles [sw13836]
  • ARTS: alignment of RNA tertiary structures, ARTS is a fully automated method for aligning ... pair of nucleic acid 3D structures (RNAs or DNAs) and detecting a-priori unknown common ... thousands of nucleotides or small local tertiary motifs with at least two successive base pairs ... structure. Recently, ARTS was used to construct the DARTS classification database of all solved RNA...
  • FRASS

  • Referenced in 2 articles [sw15707]
  • novel RNA structures, during the past few years, demands automated methods for structure comparison. While ... many algorithms handle only small motifs, few techniques, developed in recent years, (ARTS, DIAL, SARA ... available for the structural comparison of large and intact RNA molecules. Results: The FRASS...