Piatkowski Pawel, Jablonska Jagoda, Zyla Adriana, Niedzialek Dorota, Matelska Dorota, Jankowska Elzbieta, Walen Tomasz, Dawson Wayne K, Bujnicki Janusz M
Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland.
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland.
Nucleic Acids Res. 2017 Sep 19;45(16):e150. doi: 10.1093/nar/gkx631.
RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure. Comparing and classifying macromolecular 3D structures is of crucial importance for structure-based function inference and it is used in the characterization of functional motifs and in structure prediction by comparative modeling. However, compared to the numerous methods for protein structure superposition, there are few tools dedicated to the superimposing of RNA 3D structures. Here, we present SupeRNAlign (v1.3.1), a new method for flexible superposition of RNA 3D structures, and SupeRNAlign-Coffee-a workflow that combines SupeRNAlign with T-Coffee for inferring structure-based sequence alignments. The methods have been benchmarked with eight other methods for RNA structural superposition and alignment. The benchmark included 151 structures from 32 RNA families (with a total of 1734 pairwise superpositions). The accuracy of superpositions was assessed by comparing structure-based sequence alignments to the reference alignments from the Rfam database. SupeRNAlign and SupeRNAlign-Coffee achieved significantly higher scores than most of the benchmarked methods: SupeRNAlign generated the most accurate sequence alignments among the structure superposition methods, and SupeRNAlign-Coffee performed best among the sequence alignment methods.
人们发现RNA在多种生物过程中发挥着越来越重要的作用。大多数非编码RNA分子的功能取决于其结构。比较和分类大分子的三维结构对于基于结构的功能推断至关重要，并且它被用于功能基序的表征以及通过比较建模进行结构预测。然而，与众多蛋白质结构叠加方法相比，专门用于RNA三维结构叠加的工具很少。在这里，我们展示了SupeRNAlign（v1.3.1），一种用于RNA三维结构灵活叠加的新方法，以及SupeRNAlign-Coffee——一种将SupeRNAlign与T-Coffee相结合以推断基于结构的序列比对的工作流程。这些方法已经与其他八种RNA结构叠加和比对方法进行了基准测试。该基准测试包括来自32个RNA家族的151个结构（总共1734个成对叠加）。通过将基于结构的序列比对与Rfam数据库中的参考比对进行比较，评估叠加的准确性。SupeRNAlign和SupeRNAlign-Coffee的得分明显高于大多数基准测试方法：SupeRNAlign在结构叠加方法中生成了最准确的序列比对，而SupeRNAlign-Coffee在序列比对方法中表现最佳。
