Bioinformatics Group, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany.
Nucleic Acids Res. 2012 Jul;40(Web Server issue):W49-53. doi: 10.1093/nar/gks491. Epub 2012 Jun 11.
Due to recent algorithmic progress, tools for the gold standard of comparative RNA analysis, namely Sankoff-style simultaneous alignment and folding, are now readily applicable. Such approaches, however, compare RNAs with respect to a simultaneously predicted, single, nested consensus structure. To make multiple alignment of RNAs available in cases, where this limitation of the standard approach is critical, we introduce a web server that provides a complete and convenient interface to the RNA structure alignment tool 'CARNA'. This tool uniquely supports RNAs with multiple conserved structures per RNA and aligns pseudoknots intrinsically; these features are highly desirable for aligning riboswitches, RNAs with conserved folding pathways, or pseudoknots. We represent structural input and output information as base pair probability dot plots; this provides large flexibility in the input, ranging from fixed structures to structure ensembles, and enables immediate visual analysis of the results. In contrast to conventional Sankoff-style approaches, 'CARNA' optimizes all structural similarities in the input simultaneously, for example across an entire RNA structure ensemble. Even compared with already costly Sankoff-style alignment, 'CARNA' solves an intrinsically much harder problem by applying advanced, constraint-based, algorithmic techniques. Although 'CARNA' is specialized to the alignment of RNAs with several conserved structures, its performance on RNAs in general is on par with state-of-the-art general-purpose RNA alignment tools, as we show in a Bralibase 2.1 benchmark. The web server is freely available at http://rna.informatik.uni-freiburg.de/CARNA.
由于最近算法上的进展，用于 RNA 比较分析的金标准工具，即 Sankoff 风格的同时对齐和折叠，现在已经可以方便地应用了。然而，这些方法是根据同时预测的单个嵌套共识结构来比较 RNA 的。为了在标准方法的这种限制至关重要的情况下，使 RNA 的多重比对可用，我们引入了一个网络服务器，该服务器为 RNA 结构比对工具“CARNA”提供了一个完整且方便的接口。该工具独特地支持每个 RNA 具有多个保守结构的 RNA，并内在地对齐假结；这些功能对于对齐核糖开关、具有保守折叠途径的 RNA 或假结非常理想。我们将结构输入和输出信息表示为碱基对概率点图；这为输入提供了很大的灵活性，范围从固定结构到结构集合，并能够立即对结果进行可视化分析。与传统的 Sankoff 风格方法相比，“CARNA”同时优化输入中的所有结构相似性，例如跨越整个 RNA 结构集合。即使与已经昂贵的 Sankoff 风格对齐相比，“CARNA”通过应用先进的基于约束的算法技术，解决了一个本质上更难的问题。尽管“CARNA”专门用于对齐具有几个保守结构的 RNA，但我们在 Bralibase 2.1 基准测试中表明，它在一般 RNA 对齐工具方面的性能与最先进的通用 RNA 对齐工具相当。该网络服务器可免费在 http://rna.informatik.uni-freiburg.de/CARNA 上获得。
