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CATUI Data Sources

Table of Contents

1. Introduction (Back to Top)

2. File-Based Sequence Alignments

An important development goal for the CATUI Alignment Viewer is to support many different sequence formats including translation between compatible formats. Currently, the CATUI Alignment Viewer only supports visualization of RNA and DNA sequences. As development continues, and new formats are added, this section will be updated to document:
  1. CATUI Features Supported by Format
  2. Translation Support

2a. FASTA Alignments (Back to Top)

CATUI Features Supported
  1. Simultaneous Alignment Views (link)
  2. Reference Sequences (link)
  3. Workspaces (link)
Translation Support

3. rCAD-Based Sequence Alignments (Back to Top)

The CATUI Alignment Viewer now supports the visualization of RNA and DNA sequence alignments stored in the rCAD Database Reference Implementation (link). To open any RNA sequence alignment from an rCAD database, the user must first configure a connection. It is possible to configure multiple connections to the same rCAD database and even the same RNA sequence alignment. Connections can be included in Workspaces or saved independently.

Each connection to rCAD database and a specific RNA sequence alignment is based on a set of properties. The properties used to configure a connection to an rCAD database and a specific RNA sequence alignment are:
  1. Connection Name
  2. rCAD Database Server
  3. rCAD Database Name
  4. Authentication
  5. Sequence Type - The type of sequences (Ribosomal RNA, Transfer RNA, etc) in the alignment to open.
  6. Alignment Name
  7. Cell Location - Usually set to all locations unless a user wants to restrict the view to sequences from only a specific location.
  8. Evolutionary Relationships - The root taxonomy container for the view. For example I could restrict my view to only include Archaea sequences.

CATUI Features Supported
  1. Simultaneous Alignment Views (link)
  2. Grouping by Evolutionary Relationships (link)
  3. Reference Sequences (link)
  4. Workspaces (link)
Translation Support

3a. Opening a new rCAD Alignment Connection (Back to Top)

  • To open an rCAD alignment connection, right-click on the Sequence Alignments data source category and open an RCAD Database (RI)
CATUI rCAD Data Source Connection Configuration
  • Step 1: Enter the rCAD database connection information, use the Tab key or the mouse to move between fields. When finished, click the Next button.
    1. Connection Name: Any name you want
    2. Server
      1. rCAD Server on the Same Computer, Default Instance: Use (local) or "."
      2. rCAD Server on the Same Computer, Default Instance w/SQL Express: Use .\SQLEXPRESS
      3. rCAD Server on Different Computer: Use hostname\instancename. For example, if your rCAD database is on a server named foo and the instance name was bar, you would use foo\bar.
    3. Database: Select the database that corresponds to the rCAD database you want to use.
    4. Login Details
      1. Windows Authentication: Use if your rCAD database is on the same computer you are using the CATUI on and your Windows login has access to the rCAD database.
      2. SQL Authentication: Use if your rCAD database is on a different computer and/or you have either been assigned or created a specific rCAD database login.
    5. Remember this Connection: Check this option to have the CATUI save this connection configuration for future visits.
CATUI rCAD Data Source Connection Configuration
  • Step 2: Continue configuring the rCAD database connection by identifying the sequence alignment to visualize. When finished, click the Next button to begin processing the connection.
    1. Sequence Type: This field acts as a filter on the Alignment field below.
    2. Alignment: The specific alignment to open from the rCAD database.
    3. Cell Location: Default is All Cell Locations, use this to restrict the view of the alignment to only sequences from a specific cell location.
    4. Taxonomy Selection: Use this to restrict the view of the alignment to only sequences from certain branches of the phylogenetic tree. In the example below, I am restricting my view to Archaea sequences.
CATUI rCAD Data Source Connection Configuration
  • When the connection is finished processing, it will appear as a new data source and is ready to visualize.
CATUI rCAD Data Source Connection Configuration

3b. Changing an open rCAD Alignment Connection (Back to Top)

  • All properties of an open rCAD Alignment Connection can be changed at any time. Right-click on the rCAD Connection and select Properties
  • The most useful property to change is the Taxonomy Selection. For example, if the connection was initially limited to only Archaea sequences, I could now change it to all Cellular Organisms by changing the Taxonomy Selection for the connection.
CATUI rCAD Data Source Connection Configuration

3c. Opening a saved rCAD Alignment Connection (Back to Top)

  • Once at least one rCAD Alignment Connection is configured to be saved, the CATUI will always prompt to open saved connections before configuring a new connection.
  • Connections are saved in the installed directory in an XML file named: Bio.Data.Providers.rCADRI.SaveDB.xml. To clear all saved connections, delete this file.
  • Select the saved connection to open and select Ok. If you still want to create a new connection, select the Add New... button.
CATUI rCAD Data Source Connection Configuration

4. 2-D RNA Structure Diagrams (Back to Top)

The CATUI Secondary Structure Viewer currently supports the 2-D visualization of RNA secondary structure models. Three different visualizations are available:
  1. 2-D
  2. Circle
  3. Nested
Depending on the secondary structure input file, certain visualizations may be unavailable. Once a secondary structure model is opened, the CATUI Secondary Structure Viewer will show you which visualizations are supported.

4a. BPSEQ Format (Back to Top)

A format developed by the Gutell Lab that simply lists the base pairs in a secondary structure model. Secondary structure models in BPSEQ format can be obtained from http://www.rna.ccbb.utexas.edu/DAT/3C/Structure/index.php.

Visualizations Supported
  1. Circle
  2. Nested

4b. XRNA Format (Back to Top)

A format supported by the XRNA Secondary Structure Drawing application (http://rna.ucsc.edu/rnacenter/xrna/xrna.html).

Visualizations Supported
  1. 2-D
  2. Circle
  3. Nested

Last edited Dec 11, 2009 at 10:13 PM by kjdoshi, version 26

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