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Bioinformatics Advance Access originally published online on January 24, 2008
Bioinformatics 2008 24(4):579-580; 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.


  Abstract

Summary: Interactive examination of RNA multiple alignments for covariant mutations is a useful step in non-coding 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 Ratón, 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 Ratón can be accessed at http://biowiki.org/RnaAlignmentViewers

Contact: ihh{at}berkeley.edu

Associate Editor: Limsoon Wong

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

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