Difference between revisions of "Dot-Bracket Notation"

From Protein Prediction 2 Winter Semester 2014
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From this input a graph-like visualization of the RNA's secondary structure is created. In this representation the nodes refer to the ribonucleotides and the edges are the hydrogen bonds that connect them. The graph is connected and undirected.
 
From this input a graph-like visualization of the RNA's secondary structure is created. In this representation the nodes refer to the ribonucleotides and the edges are the hydrogen bonds that connect them. The graph is connected and undirected.
The visualization will be done using the [https://github.com/mbostock/d3/wiki/Force-Layout Force-Layout] of D3.
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The visualization is done using Cytoscape JS with a the Preset Layout. The coordinates for each nucleotide are done as in RnaViz and the radial layout of VARNA.
   
 
[[File:Rnadotbracket.png|thumb|upright=2|alt=Illustration of the desired core functionality of the secondary structure visualization.|Illustration of the desired core functionality of the secondary structure visualization.]]
 
[[File:Rnadotbracket.png|thumb|upright=2|alt=Illustration of the desired core functionality of the secondary structure visualization.|Illustration of the desired core functionality of the secondary structure visualization.]]
   
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[[File:Rnadotbracket.png|thumb|upright=2|alt=Current state of the art.|Current state of the art.]]
For an example, please have a look at the figure on the right.
 
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The figures on the right display the original aim of the visualization as well as the current state of the visualization as done by our Javascript component. The figure shows only the visualization itself, the actual Javascript component contains also a number of options which can be used to customize and edit the visualization. A link to the complete and working program can be found in the Progress-section.
   
 
= Adding Additional Functionality to the Visualization =
 
= Adding Additional Functionality to the Visualization =

Revision as of 12:37, 3 January 2015

The aim of the project is to visualize RNA secondary structures. RNAs are chains of ribonucleotides which form complex two-dimensional structures through the formation of hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.

Core Functionality

The main task of the visualization is the following:

The program gets an RNA secondary structure in Dot-Bracked (Vienna) Notation as input. This inputs consists of two strings where the first one is the RNA sequence, and the second string sequence of dots, round, and square brackets with the same length as the RNA sequence. For more information, please see Dot-Bracket Notation.

From this input a graph-like visualization of the RNA's secondary structure is created. In this representation the nodes refer to the ribonucleotides and the edges are the hydrogen bonds that connect them. The graph is connected and undirected. The visualization is done using Cytoscape JS with a the Preset Layout. The coordinates for each nucleotide are done as in RnaViz and the radial layout of VARNA.

Illustration of the desired core functionality of the secondary structure visualization.
Illustration of the desired core functionality of the secondary structure visualization.
Current state of the art.
Current state of the art.

The figures on the right display the original aim of the visualization as well as the current state of the visualization as done by our Javascript component. The figure shows only the visualization itself, the actual Javascript component contains also a number of options which can be used to customize and edit the visualization. A link to the complete and working program can be found in the Progress-section.

Adding Additional Functionality to the Visualization

After the core functionality is established, we plan to add additional functionality to the visualization. Current ideas are:

  • Display additional information on mouse-over
  • Drag nodes or even the whole visualization to enable examination of the structure from different angles
  • Make the visualization editable: Allow addition and deletion of nodes and edges and export the changes in a suited format.

Allow Different Input Formats

Dot-Bracket Notation is not the only popular way to represent RNA secondary structure. Other commonly used formats are:

Progress

Task Implemented
Core Functionality Yes
Drag nodes Yes
Display additional info on mouse-over No
Edit graph and export changes No
PBseq format compatibility No
Connect (.ct) format compatibility No

Current preliminary version of the implementation: RNA Secondary Structure Visualization

Source Code

People

Additional Links