Dot-Bracket Notation

From Protein Prediction 2 Winter Semester 2014
Revision as of 15:29, 5 December 2014 by Ppwikiuser (talk | contribs)

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 will be done using the Force-Layout of D3.

Illustration of the desired core functionality of the secondary structure visualization.
Illustration of the desired core functionality of the secondary structure visualization.

For an example, please have a look at the figure on the right.

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:


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


Additional Links