The Comparison of RNA Secondary Structures with Nested Arc-Annotation

In recent years, RNA structural comparison becomes a crucial problem in bioinformatics research. Generally, it is a popular approach for representing the RNA secondary structures with arc-annotation sets. Several methods can be used to compare two RNA structures, such as tree edit distance, longest arcpreserving common subsequence (LAPCS) and stembased alignment. However, these methods may be helpful only for small RNA structures because of their high time complexity. In this paper, we propose a simplified method to compare two RNA structures in O(mn) time, where m and n are the lengths of the two given RNA sequences, respectively. Our method transforms the RNA structures into specific sequences called object sequences, then compares these object sequences to find their common substructures. We test our comparison method with 118 RNA structures obtained from RNase P Database. For any two structures, we try to identify whether they are in the same family by both structure comparison and sequence comparison. In our experiment, we find that our method for comparing RNA structures can yield better hit rates and is faster than the traditional method to compare the RNA sequences. Therefore, our approach for comparing RNA secondary structures is more sensitive in biology and more efficient in time complexity.