C
omparative
R
NA
W
eb 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
»
3: Data
»
3C. Mass Data Retrieval
»
Secondary Structure Diagram Retrieval
Organism:
View Matching Organisms:
Phylogenetic Classification:
Archaea
Bacteria
Eukaryota
Virus
RNA Class:
5S
16S
23S
Group I Introns
Group II Introns
Cell Location:
Mitochondrion
Nucleus
Chloroplast
Cyanelle
File Format:
PostScript
PDF
BPSEQ
To start your search, you can type in an organism name (part or all) and/or mark some checkboxes.
Notes:
To download all the available secondary structures, make no selections and submit.
To download all the secondary structures belonging to a group (by any of: Phylogenetic Classification, Cell Location, or RNA Class), select that particular group and submit.
You may also use more than one restriction. For example, if you want only Eukaryotic Mitochondrion 16S secondary structures, check Eukaryota, Mitochondrion, and 16S, and then submit.
For Organism searches:
To get the secondary structure of an organism, type the name of the organism in the text field and submit.
If you are not sure about the complete name of the organism, do the following (assume that you want the secondary structure of
Escherichia coli
):
Type a part of the name (e.g : coli) and click the "V" button.
A list of organism names (for which the secondary structure is available) which contain the pattern "coli" wiil be displayed below the search box.
Click on
Escherichia coli
and submit.