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.

中文翻译：

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SupeRNAlign：一种新工具，可灵活叠加同源RNA结构并推断出基于结构的准确序列比对

已经发现RNA在多种生物学过程中起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。对基于分子的3D结构进行比较和分类对于基于结构的功能推断至关重要，它可用于功能基序的表征以及通过比较建模进行的结构预测中。但是，与用于蛋白质结构叠加的多种方法相比，很少有专门用于RNA 3D结构叠加的工具。在这里，我们介绍SupeRNAlign（v1.3.1）（一种可灵活叠加RNA 3D结构的新方法）和SupeRNAlign-Coffee（一种将SupeRNAlign与T-Coffee结合以推断基于结构的序列比对的工作流程）。该方法已与其他八种RNA结构重叠和比对方法进行了比较。基准测试包括来自32个RNA家族的151个结构（总共1734个成对重叠）。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，可以评估叠加的准确性。SupeRNAlign和SupeRNAlign-Coffee的得分远高于大多数基准测试方法：SupeRNAlign在结构叠加方法中产生了最准确的序列比对，而SupeRNAlign-Coffee在序列比对方法中表现最好。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，可以评估叠加的准确性。SupeRNAlign和SupeRNAlign-Coffee的得分远高于大多数基准测试方法：SupeRNAlign在结构叠加方法中产生了最准确的序列比对，而SupeRNAlign-Coffee在序列比对方法中表现最好。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，可以评估叠加的准确性。SupeRNAlign和SupeRNAlign-Coffee的得分远高于大多数基准测试方法：SupeRNAlign在结构叠加方法中产生了最准确的序列比对，而SupeRNAlign-Coffee在序列比对方法中表现最好。