• Rnall

  • Referenced in 1 article [sw23119]
  • information of RNA local secondary structures (LSSs) can help retrieve biologically important motifs and study...
  • ARTS

  • Referenced in 6 articles [sw13836]
  • ARTS: alignment of RNA tertiary structures, ARTS is a fully automated method for aligning ... even thousands of nucleotides or small local tertiary motifs with at least two successive base ... DARTS classification database of all solved RNA 3D structures...
  • SARSA

  • Referenced in 4 articles [sw13834]
  • structures and MARTS for multiple alignment of RNA tertiary structures. Particularly in PARTS, we have ... structural motifs, (iii) local alignment for finding locally similar substructures and (iv) normalized local alignment ... effect of local alignment. Both tools in SARSA take as input RNA 3D structures...
  • iPARTS

  • Referenced in 4 articles [sw13839]
  • structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format ... structural motifs or substructures), local alignments (for finding locally similar substructures) and normalized local structural ... alignments (for identifying more similar local substructures without non-similar internal fragments), with graphical display ... rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online...
  • DARN!

  • Referenced in 4 articles [sw00186]
  • Darn is a RNA motif search tool. It finds all the subsequences that match ... Darn uses a weighted constraint solver to localize the portions of a genomic sequencethat match...
  • DIAL

  • Referenced in 6 articles [sw13837]
  • algorithm for pairwise 3D structural alignment of RNA. DIAL achieves quadratic time by performing ... global (Needleman–Wunsch), local (Smith–Waterman) and semiglobal (modified to yield motif search). Suboptimal alignments ... user-specified 3D motif. The query motif may be contiguous in the linear chain ... semiglobal motif search may be of most interest in attempts to identify RNA motifs. DIAL...
  • Locomotif

  • Referenced in 3 articles [sw35380]
  • established, but informal way in which RNA motifs are communicated in the literature. Thus ... client-server approach. Motifs are designed by the user locally. Search programs are generated...
  • ATtRACT

  • Referenced in 1 article [sw29373]
  • motifs. RNA-binding proteins (RBPs) play a crucial role in key cellular processes, including RNA ... RBPs and RNA is key to improve our knowledge of RNA processing, localization and regulation ... resource that includes information on experimentally validated motifs, RBPs and integrated tools to exploit this ... RBPs and 1583 RBP consensus binding motifs, 192 of which are not present...
  • 3DNA

  • Referenced in 4 articles [sw21991]
  • other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines ... rigorous matrix-based scheme to calculate local conformational parameters and rebuild the structure from these...
  • RNABC

  • Referenced in 1 article [sw10929]
  • local geometry problems. Its input is an all-atom coordinate file for an RNA crystal ... effectiveness of RNABC, first on the S-motifs from 42 RNA structures, and second ... outliers) in 25 unrelated RNA structures. Among the 101 S-motifs, 88 had diagnosed problems ... after examining electron density (where available) and local conformation. Thus, even for these worst cases...
  • VaZyMolO

  • Referenced in 1 article [sw16899]
  • fold-homology studies. The ‘viral enzyme module localization’ (VaZyMolO) tool has been developed, which aims ... both negative- and positive-sense, single-stranded RNA viruses available from NCBI. In VaZyMolO ... convergence of results from sequence composition analysis, motif search, transmembrane region search and domain definitions...
  • Matlab

  • Referenced in 13100 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • mclust

  • Referenced in 281 articles [sw00563]
  • R package mclust: Normal Mixture Modeling for Model...
  • R

  • Referenced in 9188 articles [sw00771]
  • R is a language and environment for statistical...
  • Bioconductor

  • Referenced in 312 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • MASS (R)

  • Referenced in 314 articles [sw04479]
  • R package MASS: Support Functions and Datasets for...
  • LIBSVM

  • Referenced in 1155 articles [sw04879]
  • LIBSVM is a library for Support Vector Machines...
  • WEKA

  • Referenced in 299 articles [sw06435]
  • WEKA: Waikato Environment for Knowledge Analysis. WEKA is...