Introduction

Structured functional RNAs are conserved on the level of secondary and tertiary structure, rather than at sequence level, and so traditional sequence-based searches often fail to identify them. Structure-based searches are increasingly used to discover known RNA motifs in sequence databases. We describe the application of the program RNABOB, which performs such searches by allowing the user to define a desired motif's sequence, paired and spacer elements and then scans a sequence file for regions capable of assuming the prescribed fold. Structure descriptors of stem-loops, internal loops, three-way junctions, kissing loops, and the hammerhead and hepatitis delta virus ribozymes are shown as examples of implementation of structure-based searches.

Publications

  1. Computational discovery of folded RNA domains in genomes and in vitro selected libraries.
    Cite this
    Riccitelli NJ, Lupták A, 2010-10-01 - Methods (San Diego, Calif.)

Credits

  1. Nathan J Riccitelli
    Developer

    University of California, Department of Chemistry, United States of America

  2. Andrej Lupták
    Investigator

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Summary
AccessionBT006610
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAndrej Lupták