RNA Comparative Analysis Software Tools Version 2.0

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

Note: There appears to be a bug with the way the built in unzip tool in Windows 7 is handling the CATUI3.0.zip file. Use WinZip or 7zip to extract.

The RNA Comparative Analysis Software tools is an advanced software infrastructure for the high-throughput Comparative Analysis of RNA sequences and structure.

The RNA Comparative Analysis Software tools consist of two major components:

RNA Comparative Analysis Database (rCAD)

• Current Version: rCAD Reference Implementation 1.0

Comparative Analysis Toolkit User Interface (CATUI)

• Current Version: CATUI 3.0.
• Can be installed standalone.

Minimum Installation Prerequisites:

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

CATUI Version 3.00.00 (Back to Top)

• Note: The CATUI is not currently functional for sequence alignment editing work, but is functional for sequence alignment visualization.
• CATUI Installation instructions available here.
• CATUI 3.0 Documentation is integrated in the application, access with the F1 key.
• CATUI 3.0 Discussion Thread is available here.

CATUI 3.00 Data Sets:

• RNA alignments available at: http://www.rna.ccbb.utexas.edu/DAT/3C/Alignment/. Select alignments in FASTA format (alnFA).
• 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 1.0

Design Highlights over CATUI 2.0

• More consistent Windows Look and Feel
  • Keyboard Shortcuts, Menus and Toolbar
• CATUI Alignment Browser
  • Custom WPF Control with significant performance enhancements over CATUI 2.0
  • Alignment Viewer Customization and Profiles
  • Taxonomy Browser
  • Birds Eye Viewer
  • Split Screen View
  • Integrated Documentation
  • Migration to .NET 4.0

rCAD Reference Implementation Version 1.00.00 (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