RNA Comparative Analysis Software Tools

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Updated Release: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

kjdoshi — Tue, 31 Aug 2010 20:41:16 GMT

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:

Released: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

Tue, 31 Aug 2010 20:41:16 GMT

RNA Comparative Analysis Software Tools Version 3.0

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:

Updated Release: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

kjdoshi — Mon, 30 Aug 2010 17:13:24 GMT

RNA Comparative Analysis Software Tools Version 3.0

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:

Released: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

Mon, 30 Aug 2010 17:13:24 GMT

RNA Comparative Analysis Software Tools Version 3.0

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:

Source code checked in, #53568

kjdoshi — Mon, 30 Aug 2010 17:06:05 GMT

Trunk at CATUI 3.5.1, rCAD 1.5.1

Source code checked in, #53567

kjdoshi — Mon, 30 Aug 2010 16:47:00 GMT

Source code checked in, #53566

kjdoshi — Mon, 30 Aug 2010 16:46:31 GMT

Updated Release: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

kjdoshi — Mon, 30 Aug 2010 16:27:24 GMT

RNA Comparative Analysis Software Tools Version 3.0

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:

Released: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

Mon, 30 Aug 2010 16:27:24 GMT

RNA Comparative Analysis Software Tools Version 3.0

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:

Updated Wiki: Home

kjdoshi — Mon, 30 Aug 2010 15:36:27 GMT

Project Description

A software infrastructure for the Comparative Analysis of RNA. The infrastructure consists of a novel database, RNA Comparative Analysis Database (rCAD) and an application for visualization/manipulation of data from rCAD, Comparative Analysis Toolkit User Interface (CATUI).

Releases

New - RNA Comparative Analysis Tools 3.00, Released 8/19/2010
- CATUI 3.51
  - Note: - If you installed CATUI 3.5 via clickonce, you will have to uninstall it and reinstall via clickonce to get CATUI 3.51.
- rCAD Reference Implementation 1.5.1
  - Note: - If you installed rCAD 1.5.0, you will have to uninstall it and reinstall to update to rCAD 1.5.1
  - Note: - The 5S rRNA rCAD dataset at the CRW Site (http://www.rna.ccbb.utexas.edu/DAT/3C/Alignment/#CRW) is updated to included 179 2-D structure models (requires rCAD 1.5.1).
  - Note: - We have found issues related to installing the x86 version of the rCAD Utilities on x64 Windows. In particular, the rCAD Creator and rCAD Taxonomy Updater utilities will complain of Registry errors. Please install the x64 version of the rCAD Utilties on x64 Windows and the x86 on version of the rCAD Utilities on x86 Windows.

RNA Comparative Analysis Tools 2.00, Released 2/16/2010
- CATUI 3.0
  - Note: - There appears to be an issue with the way the built in unzip tool in Windows 7 is handling the CATUI3.0.zip file. Use WinZip or 7zip to extract.
  - New, 2/18/2010 - The first video tutorial, an introduction to the CATUI 3.0 is available. Head on over to the download page here to get it or visit the Gutell Lab's YouTube Page: http://www.youtube.com/GutellLab
- CATUI 3.0 Documentation
- rCAD Reference Implementation 1.0

RNA Comparative Analysis Tools 1.00, Released 1/29/2010
- CATUI 2.0
- rCAD Reference Implementation 1.0

Publications/Citing this work

1. Doshi K.J., Gutell R.R., and Ozer S. (2010)
rCAD: The RNA Comparative Analysis Database
(manuscript submitted for publication)
Note: Some of the figures on this site are adapted from that manuscript.

2. Doshi K.J., Gardner D.P., Cannone.J.J, Gutell.R.R. and Smith M. (2010)
CATUI: The Comparative Analysis Toolkit User Interface
(manuscript in preparation)

External Links

Gutell Lab Research Site:
- http://www.rna.ccbb.utexas.edu
Microsoft Research Spotlight:
- http://www.microsoft.com/mscorp/tc/determining-fundamental-principles.mspx
Computational Tools to Help Solve the Puzzle of RNA Structure
- http://research.microsoft.com/en-us/collaboration/focus/health/rna-structure.aspx
rCAD - RNA Comparative Analysis using SQL Server (video presentation):
- http://research.microsoft.com/apps/video/default.aspx?id=103865
Microsoft Biology Foundation:
- http://mbf.codeplex.com

Introduction

The Gutell Lab at The University of Texas at Austin (http://www.rna.ccbb.utexas.edu) has been successfully applying Comparative Analysis techniques to study Ribosomal RNA's amongst other RNA's (1). Comparative Analysis has been used to successfully decipher the structure of RNA molecules (2), and identify and characterize new RNA structural motifs. Successful application of Comparative Analysis for RNA involves the analysis of multiple, related dimensions of information: sequence and a sequence alignment, structure (secondary and 3-D structure), and evolutionary relationships (phylogeny).

Comparative Analysis of an RNA is an iterative process involving two distinct phases: bootstrap and curation. In the bootstrap phase, an initial set of homologous sequences (closely related evolutionarily) for the RNA of interest are aligned for maximum sequence identity and a secondary structure hypothesis is made. Selection of the initial sequence set is important; generally you need sequences with enough identity to enable a sequence based alignment, but also enough variation to observe higher-order relationships between positions (e.g., covariations). In the curation phase, more sequences are added to the data set in an iterative process. The structure model hypothesis is continually tested and accepted or refuted and revised as more evolutionarily distant sequences are added to the sequence alignment. Both the bootstrap and the curation phases require the Biologist to be involved in the analysis; however, certain steps can be streamlined and automated.

The successes of the Gutell Lab and other research groups using Comparative Analysis techniques have contributed significantly to RNA science. The tremendous increase in available biological information has created new opportunities to further decipher the structure, function and evolution of cellular components, such as Ribosomal RNA, but presents new computational challenges to obtain adequate performance and scalability. The lack of software tools capable of allowing Biologists to interactively apply Comparative Analysis to ever increasing amounts of biological information has become a significant bottleneck. The Gutell Lab has continually developed and re-develop their own custom software tools to handle the ever increasing amounts of RNA sequence and structure information. While the tools developed worked within the Gutell Lab, they were not designed for dissemination within the wider scientific community. The Gutell Lab in collaboration with Microsoft Research have started this project to develop an advanced software infrastructure for applying Comparative Analysis to large RNA datasets. These tools are to be used within the Gutell Lab, but also be made available, open source, to the scientific community.

Our Comparative Analysis software infrastructure can be broken down into two separate elements. The first element is an advanced database system, built on Microsoft SQL Server 2008, capable of organizing large amounts of biological information for efficient retrieval and multi-dimensional analysis. This database system is known as the RNA Comparative Analysis Database (rCAD) (3). The rCAD database cross-indexes several dimensions of an RNA dataset: sequence, structure, and phylogenetic/evolutionary information. The rCAD database is the first biological database system capable of storing sequence alignments down to the resolution of individual nucleotides (3). Individual rows, columns and cells in an alignment can be directly included in SQL statements along with different RNA structure and phylogenetic/evolutionary information (3). By uniting multiple dimensions of information, rCAD allows new, innovative analyses of the fundamentals of RNA such as: statistics of different RNA sequence/structure motifs (Gardner, DP et al, manuscript in preparation), http://www.rna.ccbb.utexas.edu/SAE/2D or the evolution of RNA structural elements (4).

The second element of this project is a comprehensive, interactive visualization package for analyzing and manipulating large RNA datasets using Comparative Analysis. This software package is the Comparative Analysis Toolkit User Interface (CATUI) (manuscript in preparation). We intend for the CATUI to be the most sophisticated RNA Comparative Analysis sequence and structure visualization tool available. The CATUI will interact directly with the rCAD database platform.

The CATUI will support the manipulation and editing of sequence alignments containing more than 100,000 sequences. The sequence alignments can be in files or in the rCAD database. The CATUI will provide an integrated RNA secondary structure editing widget, and advanced alignment navigation tools. Users will be able to navigate sequence alignments by taxonomy or common secondary structure. Below is a very screen capture of the visualization of integrated dimensions in the CATUI (CATUI 3.0, not available till Feb 2010). In the screen capture, a sequence alignment is opened, and the sequences grouped by evolutionary relationships. A taxonomy browser allows the user to navigate the alignment in the vertical direction and an "birds-eye" viewer allows one to move across the alignment two-dimensionally.

Sections

References

Cannone JJ, Subramanian S, Schnare MN, et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics 3:2.
Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Bio 12:301-310
Doshi KJ, Gutell RR, Ozer S (2010) rCAD: The RNA Comparative Analysis Database (manuscript submitted)
Xu W, Ozer S, Gutell R (2009) Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA. Scientific and Statistical Database Management. Berlin/Heidlberg: Springer. 200-216.

Additional Information and Credits

This project is partially funded by grants from the National Institutes of Health, GM085337 and GM067317, and Microsoft External Research.
Mark Smith of Julmar Technologies Inc. http://www.julmar.com
- Julmar Model-View-ViewModel Framework: http://mvvmhelpers.codeplex.com

Updated Release: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

kjdoshi — Mon, 30 Aug 2010 15:32:02 GMT

RNA Comparative Analysis Software Tools Version 3.0

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:

Released: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

Mon, 30 Aug 2010 15:32:02 GMT

RNA Comparative Analysis Software Tools Version 3.0

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:

Updated Release: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

kjdoshi — Fri, 27 Aug 2010 20:40:00 GMT

RNA Comparative Analysis Software Tools Version 3.0

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 3.50 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:

Released: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

Fri, 27 Aug 2010 20:40:00 GMT

RNA Comparative Analysis Software Tools Version 3.0

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 3.50 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:

Source code checked in, #53527

kjdoshi — Fri, 27 Aug 2010 20:38:29 GMT

Trunk at CATUI 3.5.1 and rCAD 1.5.1

Updated Wiki: Home

kjdoshi — Fri, 27 Aug 2010 20:21:24 GMT

Project Description

Releases

New - RNA Comparative Analysis Tools 3.00, Released 8/19/2010
- CATUI 3.51
  - Note: - If you installed CATUI 3.5 via clickonce, you will have to uninstall it and reinstall via clickonce to get CATUI 3.51.
- rCAD Reference Implementation 1.5.1
  - Note: - If you installed rCAD 1.5.0, you will have to uninstall it and reinstall to update to rCAD 1.5.1
  - Note: - The 5S rRNA rCAD dataset at the CRW Site (http://www.rna.ccbb.utexas.edu/DAT/3C/Alignment/#CRW) is updated to included 179 2-D structure models (requires rCAD 1.5.1).

RNA Comparative Analysis Tools 2.00, Released 2/16/2010
- CATUI 3.0
  - Note: - There appears to be an issue with the way the built in unzip tool in Windows 7 is handling the CATUI3.0.zip file. Use WinZip or 7zip to extract.
  - New, 2/18/2010 - The first video tutorial, an introduction to the CATUI 3.0 is available. Head on over to the download page here to get it or visit the Gutell Lab's YouTube Page: http://www.youtube.com/GutellLab
- CATUI 3.0 Documentation
- rCAD Reference Implementation 1.0

RNA Comparative Analysis Tools 1.00, Released 1/29/2010
- CATUI 2.0
- rCAD Reference Implementation 1.0

Publications/Citing this work

External Links

Gutell Lab Research Site:
- http://www.rna.ccbb.utexas.edu
Microsoft Research Spotlight:
- http://www.microsoft.com/mscorp/tc/determining-fundamental-principles.mspx
Computational Tools to Help Solve the Puzzle of RNA Structure
- http://research.microsoft.com/en-us/collaboration/focus/health/rna-structure.aspx
rCAD - RNA Comparative Analysis using SQL Server (video presentation):
- http://research.microsoft.com/apps/video/default.aspx?id=103865
Microsoft Biology Foundation:
- http://mbf.codeplex.com

Introduction

Sections

References

Cannone JJ, Subramanian S, Schnare MN, et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics 3:2.
Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Bio 12:301-310
Doshi KJ, Gutell RR, Ozer S (2010) rCAD: The RNA Comparative Analysis Database (manuscript submitted)
Xu W, Ozer S, Gutell R (2009) Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA. Scientific and Statistical Database Management. Berlin/Heidlberg: Springer. 200-216.

Additional Information and Credits

This project is partially funded by grants from the National Institutes of Health, GM085337 and GM067317, and Microsoft External Research.
Mark Smith of Julmar Technologies Inc. http://www.julmar.com
- Julmar Model-View-ViewModel Framework: http://mvvmhelpers.codeplex.com

Updated Wiki: Home

kjdoshi — Fri, 27 Aug 2010 20:14:27 GMT

Project Description

Releases

New - RNA Comparative Analysis Tools 3.00, Released 8/19/2010
- CATUI 3.51
  - Note: - If you installed CATUI 3.5 via clickonce, you will have to uninstall it and reinstall via clickonce to get CATUI 3.51.
- rCAD Reference Implementation 1.5.1
  - Note: - If you installed rCAD 1.5.0, you will have to uninstall it and reinstall to update to rCAD 1.5.1

RNA Comparative Analysis Tools 2.00, Released 2/16/2010
- CATUI 3.0
  - Note: - There appears to be an issue with the way the built in unzip tool in Windows 7 is handling the CATUI3.0.zip file. Use WinZip or 7zip to extract.
  - New, 2/18/2010 - The first video tutorial, an introduction to the CATUI 3.0 is available. Head on over to the download page here to get it or visit the Gutell Lab's YouTube Page: http://www.youtube.com/GutellLab
- CATUI 3.0 Documentation
- rCAD Reference Implementation 1.0

RNA Comparative Analysis Tools 1.00, Released 1/29/2010
- CATUI 2.0
- rCAD Reference Implementation 1.0

Publications/Citing this work

External Links

Gutell Lab Research Site:
- http://www.rna.ccbb.utexas.edu
Microsoft Research Spotlight:
- http://www.microsoft.com/mscorp/tc/determining-fundamental-principles.mspx
Computational Tools to Help Solve the Puzzle of RNA Structure
- http://research.microsoft.com/en-us/collaboration/focus/health/rna-structure.aspx
rCAD - RNA Comparative Analysis using SQL Server (video presentation):
- http://research.microsoft.com/apps/video/default.aspx?id=103865
Microsoft Biology Foundation:
- http://mbf.codeplex.com

Introduction

Sections

References

Cannone JJ, Subramanian S, Schnare MN, et al. (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron and other RNAs. BMC Bioinformatics 3:2.
Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Bio 12:301-310
Doshi KJ, Gutell RR, Ozer S (2010) rCAD: The RNA Comparative Analysis Database (manuscript submitted)
Xu W, Ozer S, Gutell R (2009) Covariant Evolutionary Event Analysis for Base Interaction Prediction Using a Relational Database Management System for RNA. Scientific and Statistical Database Management. Berlin/Heidlberg: Springer. 200-216.

Additional Information and Credits

This project is partially funded by grants from the National Institutes of Health, GM085337 and GM067317, and Microsoft External Research.
Mark Smith of Julmar Technologies Inc. http://www.julmar.com
- Julmar Model-View-ViewModel Framework: http://mvvmhelpers.codeplex.com

Updated Release: RNA Comparative Analysis Software Tools 3.0 (Aug 19, 2010)

kjdoshi — Fri, 27 Aug 2010 20:13:28 GMT

RNA Comparative Analysis Software Tools Version 3.0

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 3.50 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: