A novel representation of RNA secondary structure based on element-contact graphs

Background: Depending on their specific structures, noncoding RNAs (ncRNAs) play important roles in many biological processes. Interest in developing new topological indices based on RNA graphs has been revived in recent years, as such indices can be used to compare, identify and classify RNAs. Although the topological indices presented before characterize the main topological features of RNA secondary structures, information on RNA structural details is ignored to some degree. Therefore, it is necessity to identify topological features with low degeneracy based on complete and fine-grained RNA graphical representations. Results: In this study, we present a complete and fine scheme for RNA graph representation as a new basis for constructing RNA topological indices. We propose a combination of three vertexweighted element-contact graphs (ECGs) to describe the RNA element details and their adjacent patterns in RNA secondary structure. Both the stem and loop topologies are encoded compl...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Wenjie Shu, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang
• Keywords: BMCBI 2008, Rna Graph, RNA Secondary Structures, Topological Indices