Last modified on 28 January 2010.
Literature Reference:
Doshi K.J., Gutell R.R., and Ozer S. (2010)
rCAD: The RNA Comparative Analysis Database.
Manuscript Submitted
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 Tables and Figures:
| Table 1: Topology of Ribosomal RNA sequence alignments spanning the Tree of Life | |
| Figure 1: Schematic diagram of the two phases of the Comparative Analysis workflow: Bootstrap and Curation | TIF |
| Figure 2: The three primary dimensions of information and their relationships in an RNA Comparative Analysis dataset | TIF |
| Figure 3: Our proposed software infrastructure for high-throughput RNA Comparative Analysis | TIF |
| Figure 4: Overview of the rCAD database schema organized into compartments | TIF |
| Figure 5: The Sequence Metadata compartment of the rCAD database schema | TIF |
| Figure 6: The Evolutionary Relationships compartment of the rCAD database schema | TIF |
| Figure 7: The Sequence Alignment compartment of the rCAD database schema | TIF |
| Figure 8: SQL definitions for vAlignmentGrid and vAlignmentGridUngapped | TIF |
| Figure 9: Direct access to subsets of a sequence alignment in rCAD | TIF |
| Figure 10: The Structural Relationships compartment of the rCAD database schema | TIF |
| Figure 11: A base pair frequency structural statistic with rCAD | TIF |
| Figure 12: A hairpin loop frequency structural statistic with rCAD | TIF |
| Figure 13: Phylogenetic event counting in rCAD | TIF |
| Figure 14: CATUI Application for visualization and manipulation of sequence alignemnts in rCAD | TIF |
Supplementary Data Files:
| Text S1: Comparative models (CM) and their crystal structures (Xtal) that are current available | DOCX | PDF |
| Text S2: SQL Server DDL queries to create all entities for an rCAD database instance | DOCX | PDF |
| Text S3: SQL Server CLR procedure for projecting a secondary structure loop across a sequence alignment in rCAD | DOCX | PDF |
| Text S4: SQL Server CLR procedure for phylogenetic event counting in rCAD | DOCX | PDF |
| Text S5: XML Schema for CRW format metadata file | DOCX | PDF |
| File S6: rCAD CLR Procedure, phylogenetic event counting source code file | C# |
| File S7: rCAD CLR Procedure, loop projection structural statistic source code file | C# |
