Last modified on 25 January 2016.

Literature Reference:

Ozer S., Doshi K.J., Xu W., and Gutell R.R. (2011).
rCAD: A Novel Database Schema for the Comparative Analysis of RNA.
7th IEEE International Conference on e-Science, Stockholm, Sweden. December 5-8, 2011. pp. 15-22.
[ PM | PMC | DOI ]


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Downloads:

  • The rCAD Reference Implementation is available at our Codeplex portal.
  • Ribosomal rRNA datasets formatted to import into the rCAD Reference Implementation are available here.
  • PowerPoint presentation about rCAD (eScience 2011).

Manuscript Table and Figures:

Table 1: Topology of Ribosomal RNA sequence alignments spanning the Tree of Life. HTML
Figure 1: Overview of rCAD system. PNG
Figure 2: rCAD database schema overview. PNG
Figure 3: Schema for Sequence Metadata. PNG
Figure 4: Schema for evolutionary relationship. PNG
Figure 5: Database schema for sequence alignment. PNG
Figure 6: An example of updating alignment data. PNG
Figure 7: An exemplar SQL query for retrieving partial alignment. PNG
Figure 8: Database schema of Structure Relationships. PNG
Figure 9: Example of mapping RNA structure into database. PNG
Figure 10: Finding base pair frequency example. PNG
Figure 11: Evolutionary Event Counting example. PNG

Presentation Table and Figures:

Multiple Dimensions of Data: Data Management Re-Architecture. PNG | PDF
Discoveries and Applications: Alignment Editor: rCAD Viewport. JPG | PDF
Discoveries and Applications: Alignment Editor: Alignment Editor. JPG | PDF

rCAD-Enabled Scientific Applications:

Papers (where available) are listed chronologically within each category.

Science That Is Enabled with rCAD:

RNA Folding: Wu J.C., Gardner D.P., Ozer S., Gutell R.R. and Ren P. (2009).
Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding.
Journal of Molecular Biology, 391(4):769-783. 		[ PM | PMC | DOI ]
Gardner D.P., Ren P., Ozer S., and Gutell R.R. (2011).
Statistical Potentials for Hairpin and Internal Loops Improve the Accuracy of the Predicted RNA Structure.
Journal of Molecular Biology, 413(2):473-483. 		[ PM | PMC | DOI ]
Template-based Sequence Alignment: Gardner D.P., Xu W., Miranker D.P., Ozer S., Cannone J.J., and Gutell R.R. (2012).
An Accurate Scalable Template-based Alignment Algorithm.
Proceedings of 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2012), Philadelphia, PA. October 4-7, 2012. IEEE Computer Society, Washington, DC, USA. pp. 237-243. 		[ PM | PMC | DOI ]
Shang L., Gardner D.P., Xu W., Cannone J.J., Miranker D.P., Ozer S., and Gutell R.R. (2013).
Two Accurate Sequence, Structure, and Phylogenetic Template-Based RNA Alignment Systems.
BMC Systems Biology, 7(S4):S13. 		[ PM | PMC | DOI ]
Phylogenetic Event Counting: Xu W., Ozer S., and Gutell R.R. (2009).
Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA.
21st International Conference on Scientific and Statistical Database Management. June 2-4, 2009. Springer-Verlag. pp. 200-216. 		[ PM | PMC | DOI ]
Shang L., Xu W., Ozer S., and Gutell R.R. (2012).
Structural Constraints Identified with Covariation Analysis in Ribosomal RNA.
PLoS ONE, 7(6):e39383. 		[ PM | PMC | DOI ]
Integration of 3D Structure and Comparative Sequence Alignments with rCAD: Cannone J.J, Sweeney B.A., Petrov A.I., Gutell R.R., Zirbel C.L., and Leontis N.B. (2015).
R3D-2-MSA: the RNA 3D Structure-to-Multiple Sequence Alignment Server.
Nucleic Acids Research, 43(W1):W15-W23. 		[ PM | PMC | DOI ]
Structural Statistics: Visualization presentation at the CRW Site. CRW Site Page

Science That Will Be Enabled with rCAD:

RNA2DMap (full integration with rCAD): Xu W., Wongsa A., Lee J., Shang L., Cannone J.J., and Gutell R.R. (2011).
RNA2DMap: A Visual Exploration Tool of the Information in RNA's Higher-Order Structure.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta, GA. November 12-15, 2011. IEEE Computer Society, Washington, DC, USA. pp. 613-617. 		[ PM | PMC | DOI ]
To Integrate Into RNA2DMap: Basepair Conformations: CRW Site Page
Structural Motifs: CRW Site Page
Base Stacking: CRW Site Page
Motif Evolution: CRW Site Page
RNA-Protein Interaction: CRW Site Page
RNA 3D Structure Annotation: CRW Site Page
Sequence and Structure microheterogeneity within an organism: CRW Site Page
Phylogenetic sequence signatures: CRW Site Page
Nucleotide exchanges during evolution:  
Conservation diagrams: CRW Site Page