Bendaña Yuri R, Holmes Ian H
Department of Bioengineering, UC Berkeley, Berkeley, CA, USA.
Bioinformatics. 2008 Feb 15;24(4):579-80. doi: 10.1093/bioinformatics/btm635. Epub 2008 Jan 24.
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.
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.
对RNA多序列比对进行共变突变的交互式检查是非编码RNA序列分析中的一个有用步骤。我们展示了RNA可视化隐喻的三种并行实现方式：Colorstock，一个使用ANSI终端颜色的命令行脚本；SScolor，一个生成静态HTML页面的Perl脚本；以及Ratón，一个生成动态HTML的AJAX网络应用程序。每个工具都可用于根据二级结构对RNA比对进行着色，并在茎中直观地突出显示补偿性突变。
所有源代码均可在GPL许可下免费获取。源代码可从http://biowiki.org/RnaAlignmentViewers下载，并且可以访问Ratón的原型。
