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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 »

4D. Phylogenetic Analysis of Ribosomal RNA

  • Mollusk Mitochondria
    • Lydeard C., Holznagel W.E., Schnare M.N., and Gutell R.R. (2000).
    • Phylogenetic Analysis of Molluscan Mitochondrial LSU rDNA Sequences and Secondary Structures.
    • Molecular Phylogenetics and Evolution, 15(1):83-102.
  • Polytoma Leucoplasts
    • Vernon D., Gutell R.R., Cannone J.J., Rumpf R.W., and Birky C.W. Jr. (2001).
    • Accelerated Evolution of Functional Plastid rRNA and Elongation Factor Genes Due to Reduced Protein Synthetic Load After the Loss of Photosynthesis in the Chlorophyte Alga Polytoma.
    • Molecular Biology and Evolution, 18(9):1810-1822.
  • Tree of Life at the CRW Site
    • Zwickl D., Cannone J.J., Gutell R.R., and Hillis D.H., unpublished data.
    • Reconstructing the Tree of Life with Ribosomal RNA Sequences and Structures: Integrating Phylogeny, Computational Methods, and a RNA Database.
    • Proposal submitted to NSF, 17 May 2002.
  • ITS Structure and Phylogeny of the Asteraceae
    • Goertzen, L.R., Cannone J.J., Gutell R.R., and Jansen R.K. (2003).
    • ITS Secondary Structure Derived from Comparative Analysis: Implications for Sequence Alignment and Phylogeny of the Asteraceae.
    • Molecular Phylogenetics and Evolution, 29(2):216-234.
  • Diatom Shape
    • Alverson A.J., Cannone J.J., Gutell R.R., and Theriot E.C. (2006).
    • The Evolution of Elongate Shape in Diatoms.
    • Journal of Phycology, 42(3):655-668.
  • Monophyly of Terrestrial Adephagan Beetles
    • Maddison D.R., Moore W., Baker M.D., Ellis T.M., Ober K.A., Cannone J.J., and Gutell R.R. (2009)
    • Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae).
    • Zoologica Scripta, 38(1):43-62.
  • Diatom Nuclear SSU rDNA
    • Theriot E.C., Cannone J.J., Gutell R.R., and Alverson A.J. (2009).
    • The Limits of Nuclear-Encoded SSU rDNA for Resolving the Diatom Phylogeny.
    • European Journal of Phycology, 44(3):277-290.
  • Placement of Pseudonocardia
    • Mueller U., Ishak H., Lee J., Sen R., and Gutell R.R. (2010)
    • Placement of attine ant-associated Pseudonocardia in a global phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models.
    • Antonie van Leeuwenhoek International Journal of General and Molecular Microbiology, 98(2):195-212.
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