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Comparative RNA Web Site and Project The Gutell Lab

  • 1. CAR
    • 1. Comparative Analysis of RNA
    • 1A. Current Structure Models for Reference Organisms
    • 1B. Evolution of the Noller-Woese-Gutell 16S and 23S rRNA Comparative Structure Models
    • 1C. Simple RNA Secondary and Tertiary Structure Base Pair and Unpaired Nucleotide Definitions
    • 1D. Methods: Structure Prediction with Comparative Sequence Analysis
    • 1E. Modeling the Comparative Structure of Ribosomal RNAs in the 1980s
  • 2. SAE
    • 2. Structure and Evolution
    • 2A. RNA Structure
      • Nucleotide Frequency Data
        • Base Pairs
          • 16S rRNA Model (Table)
          • 16S rRNA Tentative (Table)
          • 16S rRNA Lousy (Table)
          • 23S rRNA Model (Table)
          • 23S rRNA Tentative (Table)
          • 23S rRNA Lousy (Table)
          • 5S rRNA Model (Table)
          • 5S rRNA Tentative (Table)
          • Group I Intron RNA Model (Table)
          • Group IIA Intron RNA Model (Table)
          • Group IIB Intron RNA Model (Table)
          • tRNA Model (Table)
        • Base Triples
          • tRNA Model (Table)
          • 16S rRNA Model (Table)
          • 16S rRNA Tentative (Table)
          • 23S rRNA Model (Table)
          • 23S rRNA Tentative (Table)
        • Single Bases
          • 16S rRNA (Table)
          • 23S rRNA (Table)
      • Nucleotide Modifications
      • Crystal Structure Information
      • See Also: 4A: Three-Dimensional Structure
    • 2B. Evolution of RNA
      • RNA Conservation Diagrams
      • RNA Microheterogeneity
      • Triman Mutation Database
  • 3. DAT
    • 3. Data
    • 3A. Indices of Metadata
      • Index of Current RNA Sequences and Structures
      • New and Updated RNA Structures
    • 3B. General Access to Metadata
      • RDBMS (Standard)
      • RDBMS (PhyloBrowser)
    • 3C. Mass Data Retrieval
      • Sequence Alignment Retrieval
      • Secondary Structure Model Diagram Retrieval
      • Structure/Basepair Information Retrieval
      • Old Secondary Structure Model Diagrams
  • 4. SIM
    • 4. Supplementary Information for Manuscripts
    • 4A. Structure
      • Accuracy (Current Opinion)
      • Minimal Ribosome
      • rRNA Introns in 3D
      • rRNA Spliceosomal Introns
      • Fragmented Mollusk
      • Hypervariable SSU rRNA
      • Structural Constraint Identification
      • Plasmodium Mitochondrion
      • Three-Dimensional Structure
    • 4B. Motifs
      • U-Turn
      • A Story
      • AA.AG@Helix.Ends
      • Lonepair Triloop
      • Basepair Conformations
      • UAA/GAN Motif
    • 4C. Folding
      • 16S Folding
      • 23S Folding
      • Mfold 3.1 Evaluation
      • Correlation of Structure Statistics
      • Coarse-Grained Model
      • Statistical Potentials
    • 4D. Phylogenetic Analysis of Ribosomal RNA
      • Mollusk Mitochondria
      • Polytoma Leucoplasts
      • Tree of Life at the CRW Site
      • ITS (Asteraceae)
      • Diatom Shape
      • Beetles Monophyly
      • Diatom Nuclear SSU rDNA
      • Placement of Pseudonocardia
    • 4E. Lateral Gene Transfer: Group I Introns
      • Red Algae / Brown Algae
      • Fungi / Red Algae
    • 4F. Computation and Software
      • rCAD: The RNA Comparative Analysis Database
      • RNA2DMap: Visual Exploration of RNA Structure
      • CRWAlign: Template-based Alignment Algorithm
      • CRWAlign2: Two Accurate Template-based Alignment Systems
      • R3D-2-MSA: Structure to Sequence Alignment Server
      • RNAMotif
      • CAT: Comparative Analysis Tool
      • Covariation Analysis
  • 5. FAM
    • 5. RNA Families
    • 5A. Ribosomal RNAs (rRNAs)
      • Small Subunit Ribosomal RNA
      • Large Subunit Ribosomal RNA
      • 5S Ribosomal RNA
  • 0. AI
    • 0. Ancillary Information
    • CRW Site: Site Overview
    • CRW Site: Site Map
    • CRW Site: General Information
      • Guidelines for Data Usage
      • Acknowledgements
      • Technical Information and Assistance
      • Revision/Update History
      • Contact the CRW Site
    • Publications
      • Robin Gutell
      • Jamie Cannone
    • Server Statistics
    • Links to Other Sites
Home » 4. Supplementary Information for Manuscripts »

4F. Computation and Software

  • RNAMotif, an RNA Secondary Structure Definition and Search Algorithm
    • Macke T.J., Ecker D.J., Gutell R.R., Gautheret D., Case D.A., and Sampath R. (2001).
    • RNAMotif, an RNA secondary structure definition and search algorithm.
    • Nucleic Acids Research, 29(22):4724-4735.
  • RNA2DMap: Visual Exploration of RNA Structure
    • Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011)
    • RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.
    • Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA., pp. 613-617.
  • rCAD: The RNA Comparative Analysis Database
    • Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011).
    • rCAD: A Novel Database Schema for the Comparative Analysis of RNA.
    • 7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp. 15-22.
  • CRWAlign: An Accurate Scalable Template-based Alignment Algorithm
    • Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012)
    • An Accurate Scalable Template-based Alignment Algorithm.
    • Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. IEEE Computer Society, Washington, DC, USA. pp. 237-243.
  • Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems
    • Shang L., Gardner D.P., Xu W., Cannone J.J., Miranker D.P., Ozer S., and Gutell R.R. (2013).
    • Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems.
    • BMC Systems Biology, 7(S4):S13.
  • R3D-2-MSA: the RNA 3D Structure-to-Multiple Sequence Alignment Server
    • Cannone J.J., Sweeney B.A., Petrov A.I., Gutell R.R., Zirbel C.L., and Leontis N.B. (2015).
    • R3D-2-MSA: the RNA 3D Structure-to-Multiple Sequence Alignment Server.
    • Nucleic Acids Research, 43(W1):W15-W23.
  • CAT: the Comparative Analysis Toolkit
    • Doshi K.J., et al.
    • Unpublished (2007).
  • Covariation Analysis
    • Links to published works.
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