Abstract
In addition to transmission of genetic codes for protein synthesis, RNA is capable of per-forming a wide range of biological functions in cells, including gene regulation, RNA modifi-cation and chromosome replication. Because the functions of RNAs are largely determined by their three dimensional (3D) structures, tools capable of efficiently and accurately comparing two RNA 3D structures are important for understanding the functions of RNA. iPARTS2 was developed by our Lab in 2016 for aligning two RNA 3D structures based on primary and ter-tiary structure information. Although iPARTS2 considers the primary and tertiary structure information, it doesn’t consider secondary structure information. In fact, several studies have shown that secondary structure information is useful to compare two RNA 3D structures. In this study, we develop an RNA pairwise structure alignment tool called iPARTS3, which con-siders the primary, secondary and tertiary structure information of the input RNAs. iPARTS3 calculates an alignment of two RNA 3D structures by the following steps. First, we use the so-called structural alphabet (SA) approach to reduce the input RND 3D structures into two SA-encoded sequences. Second, we consider the primary, secondary and tertiary structure in-formation of RNAs to design a dynamic programming algorithm that can compute an optimal alignment of the two SA-encoded sequences. Third, we apply MaxSub algorithm to the opti-mal alignment of the two SA-encoded sequences such that in the superimposition of two RNA 3D structures, the number of aligned C3’ atom is as maximum as possible. Finally, our experimental results have shown that iPARTS3 indeed has better performance than the other tools, such as iPARTS2, SARA and SETTER, in terms of the quality of structural alignment. However, in terms of the quality of RNA functional annotation, iPARTS3 is inferior to iPARTS2, but it still outperforms SARA and SETTER.