TRAVeLer: a tool for template-based RNA secondary structure visualization

BMC Bioinformatics

Software

David Hoksza¹  Richard Elias¹ 

[1] Faculty of Mathematics and Physics, Charles University, 11800, Prague, Czech Republic;

关键词: Visualization;    RNA secondary structure;    Template-based modeling;    Software tool;   

DOI  :  10.1186/s12859-017-1885-4

 received in 2017-05-29, accepted in 2017-10-31,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundVisualization 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.ResultsThis article introduces Traveler, 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.ConclusionsTraveler is 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. It is available at http://github.com/davidhoksza/traveler.

【 授权许可】

CC BY   
© The Author(s) 2017

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