RTM-align: an improved RNA alignment tool with enhanced short sequence performance via post-standardization and fragment alignment

Understanding the three-dimensional structure of RNA is crucial for studying various biological processes. Accurate alignment and comparison of RNA structures are essential for illustrating RNA functionality and evolution. The existing RNA alignment tools suffer from limitations such as size-dependency of scoring functions and inadequate handling of short RNA fragments, leading to the conflicting interpretation of structural and functional relationships among RNA molecules. Hence, we introduce RTM-align, a novel RNA structural alignment tool enhanced for short RNAs. RTM-align employs the RTM-score, which integrates post-standardization to ensure size-independence and utilizes a fragment alignment strategy that improves alignment accuracy by concentrating on structural motifs and local structural elements. Benchmarking results demonstrate that RTM-align outperforms existing tools in RNA structure comparison, offering a universal scoring scale regardless of RNA length. The improvement is particularly evident in evaluating predicted structures for CASP15 RNA targets, with significant enhancements observed for the short RNA target R1117. RTM-align is expected to significantly improve the accuracy and reliability of RNA structure alignment and comparison, thereby aiding in the deeper understanding and discovery of novel RNA functions and their interactions in biological systems. RTM-align is now available at https://github.com/BEAM-Labs/RTM-align.