Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
Nucleic Acids Res. 2020 Jul 27;48(13):e77. doi: 10.1093/nar/gkaa453.
A fast-growing number of non-coding RNA structures have been resolved and deposited in Protein Data Bank (PDB). In contrast to the wide range of global alignment and motif search tools, there is still a lack of local alignment tools. Among all the global alignment tools for RNA 3D structures, STAR3D has become a valuable tool for its unprecedented speed and accuracy. STAR3D compares the 3D structures of RNA molecules using consecutive base-pairs (stacks) as anchors and generates an optimal global alignment. In this article, we developed a local RNA 3D structural alignment tool, named LocalSTAR3D, which was extended from STAR3D and designed to report multiple local alignments between two RNAs. The benchmarking results show that LocalSTAR3D has better accuracy and coverage than other local alignment tools. Furthermore, the utility of this tool has been demonstrated by rediscovering kink-turn motif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.
越来越多的非编码 RNA 结构已被解析并存储在蛋白质数据库（PDB）中。与广泛的全局比对和模体搜索工具相比，仍然缺乏局部比对工具。在所有用于 RNA 3D 结构的全局比对工具中，STAR3D 因其前所未有的速度和准确性而成为一种有价值的工具。STAR3D 使用连续的碱基对（堆叠）作为锚点比较 RNA 分子的 3D 结构，并生成最佳的全局比对。在本文中，我们开发了一种局部 RNA 3D 结构比对工具，命名为 LocalSTAR3D，它是从 STAR3D 扩展而来的，旨在报告两个 RNA 之间的多个局部比对。基准测试结果表明，LocalSTAR3D 的准确性和覆盖率均优于其他局部比对工具。此外，通过重新发现扭结 - 转角模体实例、II 组内含子 RNA 中的保守结构域以及 IRES RNA 的 tRNA 模拟，证明了该工具的实用性。
