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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:

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 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:

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:

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

kjdoshi — Fri, 27 Aug 2010 20:12:30 GMT

RNA Comparative Analysis Software Tools Version 3.0

Current Version: rCAD Reference Implementation 1.5

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:

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

kjdoshi — Thu, 26 Aug 2010 17:57:10 GMT

RNA Comparative Analysis Software Tools Version 3.0

Note: If you installed CATUI 3.5 via clickonce before 8/26, you will need to uninstall and reinstall to update to CATUI 3.51.

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

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

RNA Comparative Analysis Database (rCAD)

Current Version: rCAD Reference Implementation 1.5

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 1.50.00 (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)

Thu, 26 Aug 2010 17:57:10 GMT

RNA Comparative Analysis Software Tools Version 3.0

Current Version: rCAD Reference Implementation 1.5

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 1.50.00 (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 — Thu, 26 Aug 2010 17:45:51 GMT

RNA Comparative Analysis Software Tools Version 3.0

Current Version: rCAD Reference Implementation 1.5

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 1.50.00 (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 — Thu, 26 Aug 2010 17:24:50 GMT

RNA Comparative Analysis Software Tools Version 3.0

Current Version: rCAD Reference Implementation 1.5

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 isintegrated 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 1.50.00 (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 — Thu, 26 Aug 2010 17:16:13 GMT

RNA Comparative Analysis Software Tools Version 3.0

Current Version: rCAD Reference Implementation 1.5

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 isintegrated 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 1.50.00 (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 — Thu, 26 Aug 2010 17:08:26 GMT

RNA Comparative Analysis Software Tools Version 3.0

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 1.5

Comparative Analysis Toolkit User Interface (CATUI)

Current Version: CATUI 3.5.
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 3.50.00 (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 isintegrated 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 1.50.00 (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 — Thu, 26 Aug 2010 15:09:12 GMT

RNA Comparative Analysis Software Tools Version 3.0

Current Version: rCAD Reference Implementation 1.5

Comparative Analysis Toolkit User Interface (CATUI)

Current Version: CATUI 3.5.
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 3.50.00 (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 isintegrated 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 1.50.00 (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)

Thu, 26 Aug 2010 15:09:12 GMT

RNA Comparative Analysis Software Tools Version 3.0

Current Version: rCAD Reference Implementation 1.5

Comparative Analysis Toolkit User Interface (CATUI)

Current Version: CATUI 3.5.
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 3.50.00 (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 isintegrated 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 1.50.00 (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: