RNA Comparative Analysis Software Tools Version 3.0

Note: If you installed CATUI 3.5 via clickonce before 8/26 or rCAD 1.5 before 8/27, you will need to uninstall and reinstall to update to CATUI 3.51 & rCAD 1.5.1 respectively.

Note: The RNA Comparative Analysis Software Tools are provided as is, without any warranty.

The RNA Comparative Analysis Software tools consist of:

RNA Comparative Analysis Database (rCAD)

• Current Version: rCAD Reference Implementation 1.5.1

Comparative Analysis Toolkit User Interface (CATUI)

• Current Version: CATUI 3.51.
• Can be installed standalone.

Minimum Installation Prerequisites:

• Microsoft Windows XP SP3, Vista, Windows 7 or Windows Server
• .NET Framework 3.5, SP1 (rCAD Utilities) and .NET Framework 4.0 (CATUI)
• rCAD: SQL Server 2008 Express Edition
• 4GB Memory

CATUI Version 3.51.00 (Back to Top)

• Note: The CATUI is not currently functional for sequence alignment editing work, but is functional for sequence alignment visualization.
• CATUI installation is now via Clickonce from Codeplex
• CATUI 3.5 Documentation is integrated in the application, access with the F1 key or from Help menu.

CATUI 3.51 Data Sets:

• RNA alignments available at: http://www.rna.ccbb.utexas.edu/DAT/3C/Alignment/. Select alignments in FASTA format (alnFA) or AE2 format.
• RNA structure models available at: http://www.rna.ccbb.utexas.edu/DAT/3C/SBPI/SBPI.xml. Select structure models in BPSEQ format.
• rCAD: Refer to the rCAD Reference Implementation 1.5

Design Highlights over CATUI 3.0

• CATUI Alignment Viewer
  • Support for AE2 format.
• CATUI Secondary Structure Editor
  • Support for RNA Secondary Structures in the following formats
    • BPSeq
    • CT
    • XRNA
    • RNAml (with extensions to support 2-D rendering properties such as colors and fonts)
    • Strml (Gutell Lab RNA Secondary Structure Model format)
  • Linked Navigation between Secondary Structure View and Alignment View when Sequence Alignment and Structure Model are in an rCAD database (version 1.5).
  • Secondary Structure Diagram generation via templating when Sequence Alignment and Template Structure Model are in an rCAD database (version 1.5).
  • Exporting a diagram to all supported Structure Model formats.

rCAD Reference Implementation Version 1.51.00 (Back to Top)

• The rCAD Utilities are provided as 32bit and 64bit binaries.
• The rCAD Reference Implementation is the rCAD database and a set of software utilities (rCAD Utilities) for creating and maintaining rCAD database instances.
• The SQL queries for the rCAD database schema are within the documentation attached to this release.
• rCAD Reference Implementation Discussion Thread is available here

rCAD Datasets:

• Pre-formatted data sets to be loaded into an rCAD database instance using the rCAD Alignment Loader utility.
• Ribosomal RNA data sets available at http://www.rna.ccbb.utexas.edu/DAT/3C/Alignment. Select from the rCAD datasets.

Installing the Reference Implementation:

• Installing the rCAD reference implementation requires first installing the rCAD Utilities.
• Then use the rCAD Creator Utility to create empty rCAD database instances.
• Finally, the rCAD Alignment Loader Utility is used to install datasets (in CRW format) into an rCAD database instance. Ribosomal RNA datasets in CRW format are available at http://www.rna.ccbb.utexas.edu/DAT/3C/Alignment.
• The CRW format is documented at: http://www.rna.ccbb.utexas.edu/AI/General/tech.

rCAD Utilities:

• rCAD Creator Utility
• rCAD Alignment Loader Utility
• rCAD Taxonomy Updater Utility