• SARSA

  • Referenced in 4 articles [sw13834]
  • used to align two or more RNA tertiary structures. The basic idea behind SARSA ... tools, PARTS for pairwise alignment of RNA tertiary structures and MARTS for multiple alignment ... RNA tertiary structures. Particularly in PARTS, we have implemented four kinds of pairwise alignments ... comparing whole structural similarity, (ii) semiglobal alignment for detecting structural motifs, (iii) local alignment...
  • 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 ... structure. Recently, ARTS was used to construct the DARTS classification database of all solved RNA...
  • iPARTS

  • Referenced in 4 articles [sw13839]
  • improved tool of pairwise alignment of RNA tertiary structures. PARTS is an improved web server...
  • ERD

  • Referenced in 1 article [sw23801]
  • conformation which is referred to as RNA tertiary structure. Since the prediction or experimental determination ... focus on the problems associated with the RNA secondary structure. This web server uses...
  • 3DNA

  • Referenced in 3 articles [sw21991]
  • other complex tertiary folding motifs found in both DNA and RNA structures. The analysis routines...
  • Assemble

  • Referenced in 1 article [sw17136]
  • analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features ... tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA...
  • MCQ4Structures

  • Referenced in 4 articles [sw15705]
  • structural similarity computation based on molecule tertiary structure representation in torsional angle space. We discuss ... structures as well as evaluation of models predicted within RNA-Puzzles contest. MCQ4Structures software...
  • RNA2D3D

  • Referenced in 1 article [sw17141]
  • primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly ... conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content ... means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement ... modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques...
  • Matlab

  • Referenced in 11969 articles [sw00558]
  • MATLAB® is a high-level language and interactive...
  • R

  • Referenced in 8180 articles [sw00771]
  • R is a language and environment for statistical...
  • STAR

  • Referenced in 12 articles [sw02515]
  • STAR: ultrafast universal RNA-seq aligner. Motivation: Accurate...
  • Bioconductor

  • Referenced in 291 articles [sw04205]
  • Bioconductor provides tools for the analysis and comprehension...
  • Rfam

  • Referenced in 32 articles [sw04637]
  • The Rfam database is a collection of RNA...
  • edgeR

  • Referenced in 46 articles [sw06936]
  • edgeR: a Bioconductor package for differential expression analysis...
  • RNAshapes

  • Referenced in 7 articles [sw07960]
  • RNAshapes: an integrated RNA analysis package based on...
  • onechannelgui

  • Referenced in 3 articles [sw07962]
  • oneChannelGUI: A graphical interface designed to facilitate analysis...
  • BaySeq

  • Referenced in 17 articles [sw10343]
  • baySeq: Empirical Bayesian analysis of patterns of differential...
  • HMMER

  • Referenced in 17 articles [sw10514]
  • HMMER web server: interactive sequence similarity searching. HMMER...
  • EMBOSS

  • Referenced in 34 articles [sw10917]
  • EMBOSS is ”The European Molecular Biology Open Software...