LocalSTAR3D: a local stack-based RNA 3D structural alignment tool.

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.