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

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F17%3A10369380" target="_blank" >RIV/00216208:11320/17:10369380 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1186/s12859-017-1885-4" target="_blank" >http://dx.doi.org/10.1186/s12859-017-1885-4</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1186/s12859-017-1885-4" target="_blank" >10.1186/s12859-017-1885-4</a>

Result language
angličtina
Original language name
TRAVeLer: a tool for template-based RNA secondary structure visualization
Original language description
Background: 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. Results: This 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. Conclusions: Traveler 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.
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Project
<a href="/en/project/GA15-00885S" target="_blank" >GA15-00885S: Novel methods for computational prediction and visualization of secondary structures of ribosomal ribonucleic acids - an integrated solution</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year
2017
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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