Last modified on 24 August 2012.

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.

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.

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