RASS: a web server for RNA alignment in the joint sequence-structure space.

Gewen He,Peixiang Zhao,Jinfeng Zhang,Anuj Srivastava,Jose Laborde,Albert Steppi

doi:10.1093/nar/gku429

Abstract

Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relationships, 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) information. Sequences and 3D structures contain non-overlapping sets of information that both determine RNA functions. When comparing RNA 3D structures, both types of information need to be taken into account. However, few methods compare RNA structures using both sequence and 3D structure information. 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 quantified 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 research community. The web server is located at http://cloud.stat.fsu.edu/RASS/.

Highlights

Comparison of ribonucleic acid (RNA) structures is an effective tool for studying the functions of RNA molecules and their evolutionary relationships
The first type of methods focuses on detection of local structural motifs to identify functional domains, such as NASSAM [9], COMPADRES [8], RNAMotifScan [11] and FR3D [7]
SARA uses a set of unit vectors derived from consecutive nucleotides to represent each nucleotide, which can be compared with other nucleotide using unit-vector root mean square (URMS) as distance [1,18]

Summary

INTRODUCTION

Comparison of ribonucleic acid (RNA) structures is an effective tool for studying the functions of RNA molecules and their evolutionary relationships. PRIMOS/AMIGOS [5] and DIAL [6] represent nucleotides with torsion angles and align the sequences encoded by the torsion angle representation These methods do not necessarily produce globally similar alignment between two RNA structures (i.e. with small RMSDs (root-mean-square-deviations)). Sequence alignment and structure alignment use different sets of information: the former uses information of side chains, which are reduced to single letters, and the latter uses information of the backbone geometry Both types of information play important roles in determining RNA functions. We develop a web server for joint sequence-structure comparison of RNA structures using ESA, called RASS (RNA alignment in the joint sequence-structure space). We first briefly describe the methodology of RASS, which is followed by a detailed description of the usage of the web server

MATERIALS AND METHODS

CONCLUSION