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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
  • 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
          • tRNA (Table)
          • 5S rRNA (Table)
          • 16S rRNA (Table)
          • 23S rRNA (Table)
          • Group I Intron (Table)
          • Group IIA Intron (Table)
          • Group IIB Intron (Table)
      • Nucleotide Modifications
      • RNAMap Secondary Structure Java Applet
      • Crystal Structure Information
    • 2B. Evolution of RNA
      • RNA Conservation Diagrams
      • RNA Signatures
      • RNA Microheterogeneity
    • 2C. Introns
      • rRNA Introns
      • Group I/II Intron Distributions
    • 2D. Structural Statistics
      • Nucleotide Statistics
      • Hairpin Statistics
      • Internal Loop Statistics
      • Internal Loop Length Statistics
  • 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
  • 4. SIM
    • 4. Supplementary Information for Manuscripts
    • 4A. Structure
      • Accuracy (Current Opinion)
      • Minimal Ribosome
      • rRNA Introns in 3D
      • rRNA Spliceosomal Introns
    • 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
    • 4D. Phylogenetic Analysis of Ribosomal RNA
      • Mollusk Mitochondria
      • Polytoma Leucoplasts
      • Tree of Life at the CRW Site
      • ITS (Asteraceae)
      • Diatom Shape
    • 4E. Lateral Gene Transfer: Group I Introns
      • Red Algae / Brown Algae
      • Fungi / Red Algae
  • 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 »

4A. Structure

  • Accuracy (Current Opinion)
    • Gutell R.R., Lee J.C., and Cannone J.J. (2002).
    • The Accuracy of Ribosomal RNA Comparative Structure Models.
    • Current Opinion in Structural Biology, 12:301-310.
  • Minimal Ribosome
    • Mears J.A., Cannone J.J., Stagg S.M., Gutell R.R., Agrawal, R.K., and Harvey S.C. (2002)
    • Modeling a Minimal Ribosome Based on Comparative Sequence Analysis.
    • Journal of Molecular Biology, 321:215-234.
  • rRNA Introns in 3D
    • Jackson S.A., Cannone J.J., Lee J.C., Gutell R.R., and Woodson S.A. (2002)
    • Distribution of rRNA Introns in the Three-Dimensional Structure of the Ribosome.
    • Running Title: rRNA Introns in 3D.
    • Journal of Molecular Biology, 323:35-52.
  • rRNA Spliceosomal Introns
    • Bhattacharya D., Simon D., Huang J., Cannone J.J., and Gutell R.R. (2003).
    • The Exon Context and Distribution of Euascomycetes rRNA Spliceosomal Introns.
    • BioMed Central Evolutionary Biology. 3:7.
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