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.
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.
Adding Additional Functionality to the Visualization
- Display nucleotide index on mouse-over
- Drag nodes and zoom in and out to enable improved examination of the structure
- Make the visualization editable: It is possible to add new hydrogen bonds. Resulting changes to the original Dot-Bracket notation of the structure will be considered automatically.
- Custom color coding of the nucleotides
Things that remain to be done
Dot-Bracket Notation is not the only popular way to represent RNA secondary structure. Other commonly used formats are:
Other things that could still be added:
- More edge types, e.g. red edges that mark pairing violations
- Better support of the IUPAC code through improved color coding
- Better support of missing sequence information, also through colors
|Dragging nodes and zooming||Yes|
|Display additional info on mouse-over||Yes|
|Edit graph and export changes||Yes, partially|
|PBseq format compatibility||No|
|Connect (.ct) format compatibility||No|
|Change nucleotide colors||Yes|
|Additional color coding for IUPAC/pairing violations/missing sequence||No|
Current preliminary version of the implementation: RNA Secondary Structure Visualization