Traveler
- Summary
- Traveler is an RNA sescondary structure visualization tool implementing a template-based approach enabling to lay out even the largest RNA structures in the standard orientation.
A separate website is maintained at https://github.com/cusbg/traveler.
Visualization of RNA secondary structures is a complex task, and, especially in the case of large RNA structures where the expected layout is largely habitual, the existing visualization tools often fail to produce suitable visualizations. This led us to the idea to use existing layouts as templates for the visualization of new RNAs similarly to how templates are used in homology-based structure prediction. Traveler is a software tool enabling visualization of a target RNA secondary structure using an existing layout of a sufficiently similar RNA structure as a template. Traveler is based on an algorithm which converts the target and template structures into corresponding tree representations and utilizes tree edit distance coupled with layout modification operations to transform the template layout into the target one. Traveler thus accepts a pair of secondary structures and a template layout and outputs a layout for the target structure. Traveler is provided as a command-line open source tool able to quickly generate layouts for even the largest RNA structures in the presence of a sufficiently similar layout.
The availability of such a tool motivated the development of a pipeline for prediction and visualization of RNA secondary structures R2DT. Currently, R2DT is maintained by RNAcentral at the EBI (European Bioniformatics Institute) and co-developed by our department. R2DT enables visualization of more then 20 million RNA structures, layout of which is now available in RNAcentral.
