Abstract
It has been realized that RNA is an important molecule in biology because it plays multiple regulated functions in the cell. Basically, functions of RNAs are largely determined by their three dimensional structures. Therefore, developing tools capable of efficiently and accurately comparing the similarity between two RNA 3D structures can help biologist to deeply realize RNA function and evolution. In 2016, our laboratory has developed a tool called iPARTS2 that aligns two RNA 3D structures based on their primary and tertiary structure information. However, iPARTS2 ignores secondary structure information in the RNAs being compared. In fact, several studies have shown that using secondary structure information to compare two RNA tertiary structures is a useful strategy. Therefore, in this study, we develop a tool called iPARTS3, which considers primary, secondary and tertiary structure information to align two RNA 3D structures. The basic steps of iPARTS3 are as follow. First, we reduce input RNA 3D structures into 1D SA-encoded sequences using the structure alphabet, which was constructed by iPARTS2 and consists of 92 elements with each element carrying both information of backbone geometry and base for a representative nucleotide. Then, we incorporate secondary structural information into these 1D SA-encoded sequences to produce arc-annotated sequences. Finally, we use traditional secondary structure alignment algorithm to compare two arc-annotated sequences can find the similarity between RNA 3D structures. Finally, our experimental results have shown that iPARTS3 indeed has better performance than iPARTS2 in terms of quality of structural alignment.