CATUI Secondary Structure Viewer

Table of Contents

1. Introduction (Back to Top)

The CATUI Secondary Structure Browser component will provide two dimensional visualization and drawing capabilities for RNA secondary structure models. The CATUI Secondary Structure Browser component will integrate with the CATUI Alignment Viewer and enable a scientist to navigate the an RNA sequence alignment using secondary structure relationships. To facilitate the create of new RNA secondary structure diagrams, the CATUI Secondary Structure Browser will enable a user to template an existing RNA secondary structure diagram from a closely related species.

The CATUI Secondary Structure Browser currently supports three different visualization modes:
  1. 2-D Visualization
  2. Circle Visualization
  3. Nested Visualization
When an RNA secondary structure model data source is supported by multiple visualization modes, the different visualizations can be opened simultaneously. For each of the visualization modes, the supported RNA secondary structure model data sources are listed.

2. Secondary Structure Visualization (Back to Top)

All secondary structure visualizations currently support zoom as well as scrolling and panning using the scrollbars and the mouse wheel. All visualizations include a status bar at the top of the window where information such as base pair or nucleotide selected is displayed. The Zoom controls are to the right of the status bar.

CATUI Status Bar
CATUI SS Browser
  • Once an RNA secondary structure model is opened as a data source, the CATUI will show the valid visualizations for the particular data source by right-clicking on the data source and selecting Show View.
CATUI SS Browser

2a. 2-D Visualization (Back to Top)

Render an RNA secondary structure model by positioning each nucleotide of the sequence individually on a 2-D diagram. The layout of the nucleotides should illustrate the major structural components (e.g., helices and unpaired regions). Additional labels are added to indicate, tertiary interactions, motifs and other structural features.

Supported Data Sources
  1. XRNA Format
CATUI SS Browser, 2-D Viz
  • Clicking any individual nucleotide identifies its index in the sequence and its 2-D x,y coordinates in the status bar.

2b. Circle Visualization (Back to Top)

Render an RNA secondary structure model as a closed circle with chords. The circle is divided equally into segments. The number of segments matches the number of nucleotides in the sequence. Interactions between nucleotides (e.g., base pairs) are represented as chords connecting the two points on the circle.

Supported Data Sources
  1. XRNA Format
  2. BPSEQ Format
CATUI SS Browser, Circle Viz
  • Clicking on any chord in the circle diagram provides base pair information in the status bar.
  • Clicking along the circle identifies individual nucleotides in the sequence in the status bar.

2c. Nested Visualization (Back to Top)

Render an RNA secondary structure model as a histogram. A continuous horizontal line forms the base of the histogram and represents the RNA sequence. Base pair interactions between nucleotides are represented as a vertical, rectangular nesting connecting the two nucleotides along the horizontal line. The height of any nesting is proportional to the number of intervening nucleotides between the 5' and 3' nucleotides of the secondary structure base pair represented by the nesting.

Supported Data Sources
  1. XRNA Format
  2. BPSEQ Format
CATUI SS Browser, Nested Viz
  • Clicking on any nesting (red line) provides base pair information in the status bar.
  • Clicking along the horizontal line identifies individual nucleotides in the sequence in the status bar.

Last edited Dec 15, 2009 at 4:38 PM by kjdoshi, version 24

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