Colorstock, SScolor, Ratón: RNA alignment visualization tools

Abstract

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.

Fig. 1.

RFAM alignment RF00165 (coronavirus 3'UTR replication element), as displayed by Colorstock (top left), SScolor (lower left) and Ratón (right). The first sequence is the reference sequence for this particular coloring. The SS_cons line displays the consensus secondary structure previously predicted by another program, such as xrate (Klosterman et al., 2006), and uploaded with the alignment (matching angle-brackets denote base-paired columns; see biowiki.org/StockholmFormat for explanation of this line). Note that the programs currently do not highlight basepairs in pseudoknots (some of which exist in this alignment).