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Colorstock, SScolor, Ratón: RNA alignment visualization tools.

Yuri R Bendaña¹, Ian H Holmes

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.

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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.

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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.