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RNA Structure01:23

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The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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RNA Secondary Structure Prediction Using High-throughput SHAPE
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TRAVeLer: a tool for template-based RNA secondary structure visualization.

Richard Elias1, David Hoksza2

  • 1Faculty of Mathematics and Physics, Charles University, Prague, 11800, Czech Republic.

BMC Bioinformatics
|November 17, 2017
PubMed
Summary

Traveler visualizes RNA secondary structures by using similar existing layouts as templates. This open-source software tool aids in generating suitable visualizations for large RNA molecules.

Keywords:
RNA secondary structureSoftware toolTemplate-based modelingVisualization

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Structural Biology

Background:

  • RNA secondary structure visualization is challenging, particularly for large structures.
  • Existing tools often struggle to generate appropriate layouts for complex RNA molecules.
  • The study proposes using homology-based template matching for RNA visualization.

Purpose of the Study:

  • Introduce Traveler, a novel software tool for RNA secondary structure visualization.
  • Enable the use of existing RNA structure layouts as templates for new visualizations.
  • Address limitations of current visualization methods for large and complex RNA structures.

Main Methods:

  • Traveler employs an algorithm to convert target and template RNA structures into tree representations.
  • Tree edit distance is utilized to compare target and template structures.
  • Layout modification operations transform the template layout to match the target structure.

Main Results:

  • Traveler generates layouts for target RNA secondary structures using template layouts.
  • The software accepts a pair of RNA secondary structures and a template layout as input.
  • It outputs a modified layout suitable for the target RNA structure.

Conclusions:

  • Traveler is an open-source, command-line tool for efficient RNA structure layout generation.
  • It effectively visualizes large RNA structures when a similar template layout is available.
  • The tool is accessible at http://github.com/davidhoksza/traveler.