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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 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 Wiki: Documentation

kjdoshi — Thu, 26 Aug 2010 17:16:37 GMT

rCAD and CATUI Documentation

Video Tutorials

CATUI 3.0 Welcome Tour (16:34, WMV) or on YouTube: http://www.youtube.com/GutellLab.

rCAD and rCAD Utilities

CATUI 3.51

Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.

CATUI 3.0

Installation
Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.
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.

CATUI 2.0

Updated Wiki: Home

kjdoshi — Thu, 26 Aug 2010 17:14:13 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

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: Documentation

kjdoshi — Wed, 25 Aug 2010 21:45:33 GMT

rCAD and CATUI Documentation

Video Tutorials

CATUI 3.0 Welcome Tour (16:34, WMV) or on YouTube: http://www.youtube.com/GutellLab.

rCAD and rCAD Utilities

CATUI 3.5

Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.

CATUI 3.0

Installation
Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.
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.

CATUI 2.0

Updated Wiki: Documentation

kjdoshi — Fri, 20 Aug 2010 15:34:32 GMT

rCAD and CATUI Documentation

Video Tutorials

CATUI 3.0 Welcome Tour (16:34, WMV) or on YouTube: http://www.youtube.com/GutellLab.

rCAD and rCAD Utilities

CATUI 3.5

CATUI 3.0

Installation
Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.
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.

CATUI 2.0

Updated Wiki: Home

kjdoshi — Thu, 19 Aug 2010 17:51:22 GMT

Project Description

Releases

New - RNA Comparative Analysis Tools 3.00, Released 8/19/2010
- CATUI 3.5
- rCAD Reference Implementation 1.5

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 — Thu, 19 Aug 2010 17:50:35 GMT

Project Description

Releases

New - RNA Comparative Analysis Tools 3.00, Released 8/19/2010

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: CATUI

kjdoshi — Wed, 24 Feb 2010 21:35:31 GMT

Comparative Analysis Toolkit User Interface (CATUI)

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)

Current Release

CATUI 3.0, Download here.
Documentation

1. Introduction
2. Architecture
3. Viewport-Based Sequence Alignment Visualization
4. Documentation Links

1. Introduction (Back to Top)

The Comparative Analysis Toolkit User Interface (CATUI) is the second major software component of the software infrastructure being developed by the Gutell Lab to support the Comparative Analysis of large RNA datasets. The CATUI is an application of the visualization and manipulation of RNA sequences and structures. The CATUI interfaces with the RNA Comparative Analysis Database (rCAD).

Through data virtualization techniques, very large RNA sequence alignments (greater than 100,000 sequences) can be efficiently visualized on a laptop computer. Alignment navigation is enhanced by utilitzing the integrated dimensions of the rCAD database (Sequence, Structure and Evolutionary Relationships. The CATUI application is a Microsoft Windows application, developed in .NET with Windows Presentation Foundation (WPF). Full documentation can be found here..

2. Architecture (Back to Top)

The CATUI application is designed to provide visualizations of the different data elements of an RNA dataset for Comparative Analysis. Currently, the CATUI has visualizations of RNA sequences (within a sequence alignment) through the Alignment Viewer and RNA secondary structures (using different structural rendering abstractions) through the Secondary Structure Viewer. Each visualization (sequence alignment or structure models) is opened in a separate window and is tied to a Data Source. Initially, all visualizations are docked in the Main Application Window.

The architecture of the CATUI is logically divided into Visualization and Data Provider components.

The Alignment Viewer and Secondary Structure Viewer components are Visualization components. The CATUI application component, BioBrowser drives the Main Application Window and has a dependency on all the Visualization components. The physical data for a RNA sequence alignment or secondary structure model is loaded by the respective Data Providers. For example, the rCAD Data Provider component loads RNA sequence alignments from the rCAD database. The Alignment Viewer component then renders the data stream from the rCAD Data Provider. The Data Providers handle all the data virtualization and implement interfaces that are utilized by the Visualization components. The Data Providers interfaces (CATUI 2.0) are provided below:

The entities provided by the Data Providers to the Visualization components are defined in the Bio.Data Component. A sequence is represented as a IBioEntity which is a list of IBioSymbol objects. Default implementations of IBioEntity and IBioSymbol are provided, or a individual data provider can implement their own.

3. Viewport-Based Sequence Alignment Visualization (Back to Top)

The Alignment Viewer scales to enable the visualization of extremely large sequence alignments using a combination of data virtualization and a viewport-driven visualization. Both of these concepts rely on the simple observation that a user is not capable of viewing an entire sequence alignment at one time one their screen. Instead, they look at a subset, which we call a viewport, of size m rows x n columns. The values for m and n are driven by: 1) the font size to rendering the alignment and 2) the size of the window.

Through data virtualization, the Alignment Viewer only caches into memory, enough data to fill the current viewport, plus some additional data around the edges that is immediately offscreen. When the viewport is moved, the Alignment Viewer updates the cache and re-renders the viewport.

Dictionary Terms

Updated Wiki: Home

kjdoshi — Mon, 22 Feb 2010 21:34:57 GMT

Project Description

Releases

New - 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: Documentation

kjdoshi — Mon, 22 Feb 2010 19:22:43 GMT

rCAD and CATUI Documentation

Video Tutorials

CATUI 3.0 Welcome Tour (16:34, WMV) or on YouTube: http://www.youtube.com/GutellLab.

rCAD and rCAD Utilities

CATUI 3.0

Installation
Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.
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.

CATUI 2.0

Updated Wiki: Home

kjdoshi — Mon, 22 Feb 2010 19:22:06 GMT

Project Description

Releases

New - 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 to PLoS Computational Biology 1/29/2010)
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 — Thu, 18 Feb 2010 23:29:52 GMT

Project Description

Releases

New - 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.
- 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 to PLoS Computational Biology 1/29/2010)
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: Documentation

kjdoshi — Thu, 18 Feb 2010 23:27:59 GMT

rCAD and CATUI Documentation

Video Tutorials

CATUI 3.0 Welcome Tour (16:34, WMV)

rCAD and rCAD Utilities

CATUI 3.0

Installation
Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.
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.

CATUI 2.0

Updated Wiki: Documentation

kjdoshi — Thu, 18 Feb 2010 22:01:34 GMT

rCAD and CATUI Documentation

Video Tutorials

CATUI 3.0 Welcome Tour (16:34, WMV)

rCAD and rCAD Utilities

CATUI 3.0

Installation
Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.
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.

CATUI 2.0

Updated Wiki: Home

kjdoshi — Wed, 17 Feb 2010 16:45:49 GMT

Project Description

Releases

New - 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.
- 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 to PLoS Computational Biology 1/29/2010)
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 — Wed, 17 Feb 2010 16:45:32 GMT

Project Description

Releases

New - RNA Comparative Analysis Tools 2.00, Released 2/16/2010
- CATUI 3.0
- CATUI 3.0 Documentation
  - 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.
- 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 to PLoS Computational Biology 1/29/2010)
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 — Tue, 16 Feb 2010 23:05:29 GMT

Project Description

Releases

New - 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.
- 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 to PLoS Computational Biology 1/29/2010)
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: Documentation

kjdoshi — Tue, 16 Feb 2010 23:03:44 GMT

rCAD and CATUI Documentation

Video Tutorials

Coming Soon!

rCAD and rCAD Utilities

CATUI 3.0

Installation
Documentation is now in a compiled help file, CATUI.chm and can be downloaded separately or accessed from within the CATUI application with the F1 key.
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.

rcat Wiki & Documentation Rss Feed

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Additional Information and Credits

Updated Wiki: Home

Project Description

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External Links

Introduction

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References

Additional Information and Credits

Updated Wiki: Home

Project Description

Releases

Publications/Citing this work

External Links

Introduction

Sections

References

Additional Information and Credits

Updated Wiki: Documentation

rCAD and CATUI Documentation

Video Tutorials

Updated Wiki: Home

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Updated Wiki: Documentation

rCAD and CATUI Documentation

Video Tutorials

Updated Wiki: Documentation

rCAD and CATUI Documentation

Video Tutorials

Updated Wiki: Home

Project Description

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External Links

Introduction

Sections

References

Additional Information and Credits

Updated Wiki: Home

Project Description

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Publications/Citing this work

External Links

Introduction

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References

Additional Information and Credits

Updated Wiki: CATUI

Comparative Analysis Toolkit User Interface (CATUI)

Current Release

Table of Contents

1. Introduction (Back to Top)

2. Architecture (Back to Top)

3. Viewport-Based Sequence Alignment Visualization (Back to Top)

Updated Wiki: Home

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Publications/Citing this work

External Links

Introduction

Sections

References

Additional Information and Credits