Introduction

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/.

Publications

  1. RASS: a web server for RNA alignment in the joint sequence-structure space.
    Cite this
    He G, Steppi A, Laborde J, Srivastava A, Zhao P, Zhang J, 2014-07-01 - Nucleic acids research

Credits

  1. Gewen He
    Developer

    Department of Computer Science, Florida State University, United States of America

  2. Albert Steppi
    Developer

    Department of Statistics, Florida State University, United States of America

  3. Jose Laborde
    Developer

    Department of Statistics, Florida State University, United States of America

  4. Anuj Srivastava
    Developer

    Department of Statistics, Florida State University, United States of America

  5. Peixiang Zhao
    Developer

    Department of Computer Science, Florida State University, United States of America

  6. Jinfeng Zhang
    Investigator

    Department of Statistics, Florida State University, United States of America

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Summary
AccessionBT006807
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByJinfeng Zhang