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Bioinformatics Advance Access published online on January 24, 2008
Bioinformatics, doi:10.1093/bioinformatics/btm635
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Colorstock, SScolor, Ratón: RNA Alignment Visualization Tools

Yuri R. Bendaña and Ian H. Holmes *

Department of Bioengineering, UC Berkeley, Berkeley, CA, USA

*to whom correspondence should be addressed. Dr. Ian Holmes E-mail: ihh{at}berkeley.edu


  Abstract

Summary: Interactive examination of RNA multiple alignments for covariant mutations is a useful step in noncoding RNA sequence analysis. We present three parallel implementations of an RNA visualization metaphor: Colorstock, a command-line script using ANSI terminal color; SScolor, a Perl script that generates static HTML pages; and Rat ón, an AJAX web application generating dynamic HTML. Each tool can be used to color RNA alignments by secondary structure and to visually highlight compensatory mutations in stems.

Availability: All source code is freely available under the GPL. The source code can be downloaded and a prototype of Rat ón can be accessed at http://biowiki.org/RnaAlignmentViewers

Contact: ihh{at}berkeley.edu

Associate Editor: Dr. Limsoon Wong

Received on October 22, 2007; revised on December 11, 2007; accepted on December 22, 2007

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