RNA Comparative Analysis Software Tools Version 1.0

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

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 2.0.
• Can be installed standalone.

Minimum Installation Prerequisites:

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

Recommended Prerequisites:

• CATUI: 3-D Discrete Graphics Card
• Server grade processor (Intel Xenon or equivalent)
• >4GB Memory
• rCAD: Internet access (for the rCAD Taxonomy Updater Utility)
• rCAD: SQL Server 2008 Standard Edition or higher and Integration Services

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

CATUI Version 2.00.00 (Back to Top)

• Note: The CATUI is not currently functional for sequence alignment editing work, but is functional for sequence alignment visualization.
• There appears to be an issue with the CATUI 2.0 on computers with .NET 4.0, Beta 2 installed. We do not know the source of the incompatibility, but the CATUI application crashes on startup.
• CATUI Installation instructions available here.
• CATUI 2.0 Documentation is available in the Documentation section.
• CATUI 2.0 Discussion Thread is available here.

CATUI 2.00 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 1.0:

• CATUI Alignment Browser
  • Rendering of alignments stored in rCAD
  • Sorting sequences in an alignment visualization by Taxonomy (rCAD alignments)
  • Setting reference sequences