Last modified on 29 August 2011.

NOTE: This section is under development.

Data Categories:

• Sequence-Level Data
• Alignment-Level Data
• Structure-Level Data
• Gutell Lab Manuscript Links

Sequence-Level Data: [Back to Top]

• FUTURE: sequences
• Current Sequence Metadata
• FUTURE: intron sites
• Nucleotide Modifications

Alignment-Level Data: [Back to Top]

• Sequence Alignments:
  • rRNA Primary Alignments
  • rRNA Seed Alignments
  • Specialized Alignments
  • rCAD Datasets
  • Alignments Used in Specific Analyses
• FUTURE: alignment metadata
• FUTURE: intron sites
• Sequence Conservation Diagrams
• Nucleotide Frequency
• Structural Statistics
• Signature Nucleotides
• Microheterogeneity
• RNA2DMap

Structure-Level Data: [Back to Top]

• Reference Structure Diagrams
• Secondary Structure (Covariation) Model Diagrams:
  • Current 16S rRNA Structures
  • New and Updated Secondary Structure Diagrams
  • Old Secondary Structure Model Diagrams
• rRNA Structure/Basepair Information
• FUTURE: 3D structures
• Structural Statistics
• Comparison of Secondary Structure Model to 3D Structure
• RNA2DMap
• Structure Motif Data

Gutell Lab Manuscript Links: [Back to Top]

• The Accuracy of Ribosomal RNA Comparative Structure Models
• Modeling a Minimal Ribosome Based on Comparative Sequence Analysis
• Distribution of rRNA Introns in the Three-Dimensional Structure of the Ribosome
• The Exon Context and Distribution of Euascomycetes rRNA Spliceosomal Introns
• Fragmentation of Ribosomal RNA Genes in Oyster Mitochondrial Genomes
• Predicting U-turns in Ribosomal RNA with Comparative Sequence Analysis
• A Story: Unpaired Adenosines in Ribosomal RNAs
• AA.AG@Helix.Ends: A:A and A:G Base-pairs at the Ends of 16 S and 23 S rRNA Helices
• The Lonepair Triloop: A New Motif in RNA Structure
• Diversity of Basepair Conformations and Their Occurrence in rRNA Structure and RNA Structural Motifs
• The UAA/GAN Internal Loop Motif: A New RNA Structural Element That Forms a Cross-strand AAA Stack and Long-range Tertiary Interactions
• A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs
• Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
• 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
• The Evolution of Elongate Shape in Diatoms
• Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)
• The Limits of Nuclear-Encoded SSU rDNA for Resolving the Diatom Phylogeny
• Placement of attine ant-associated Pseudonocardia in a global phylogeny (Pseudonocardiaceae, Actinomycetales): a test of two symbiont-association models