Comparative RNA Web Site and Project The Gutell Lab

CRW Site - Site Map

1. CAR:  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:  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:  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:  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:  RNA Families
• 5A. Ribosomal RNAs (rRNAs)
  • Small Subunit Ribosomal RNA
  • Large Subunit Ribosomal RNA
  • 5S Ribosomal RNA
0. AI:  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

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