Abstract

Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relation-ships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) in-formation. Sequences and 3D structures contain non-overlapping sets of information that both deter-mine RNA functions. When comparing RNA 3D struc-tures, both types of information need to be taken into account. However, few methods compare RNA struc-tures using both sequence and 3D structure infor-mation. Recently, we have developed a new method based on elastic shape analysis (ESA) that compares RNA molecules by combining both sequence and 3D structure information. ESA treats RNA structures as 3D curves with sequence information encoded on additional coordinates so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quanti-fied by a formal distance, geodesic distance. In this study, we implement a web server for the method, called RASS, to make it publicly available to re-search community. The web server is located at