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Published on: August 15, 2019
Colorstock, SScolor, Ratón: RNA alignment visualization tools.
1Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.
Bioinformatics (Oxford, England)
|January 26, 2008
Summary
We developed three RNA alignment viewers to analyze covariant mutations in non-coding RNA sequences. These tools visualize RNA secondary structures and highlight compensatory mutations, aiding sequence analysis.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- Interactive analysis of RNA multiple alignments is crucial for understanding non-coding RNA sequence function.
- Covariant mutations within RNA structures provide insights into functional constraints.
Purpose of the Study:
- To present three novel implementations for visualizing RNA alignments and identifying compensatory mutations.
- To facilitate the interactive examination of RNA secondary structures and mutation patterns.
Main Methods:
- Development of three parallel RNA visualization tools: Colorstock (command-line, ANSI color), SScolor (static HTML), and Ratón (dynamic AJAX web application).
- Implementation of secondary structure coloring and highlighting of compensatory mutations within RNA stems.
Main Results:
- Successfully created three distinct tools for RNA alignment visualization, catering to different user preferences and technical environments.
- Demonstrated the capability of the tools to effectively color RNA alignments by secondary structure and highlight compensatory mutations.
Conclusions:
- The presented RNA alignment viewers offer valuable methods for interactive analysis of non-coding RNA sequences.
- These tools enhance the ability to detect and interpret covariant mutations, contributing to RNA sequence analysis and functional prediction.
