Ribozymes pp 145-158 | Cite as

Discovery of RNA Motifs Using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences

  • Randi M. Jimenez
  • Ladislav Rampášek
  • Broňa Brejová
  • Tomáš Vinař
  • Andrej Lupták
Part of the Methods in Molecular Biology book series (MIMB, volume 848)


The enormous impact of noncoding RNAs on biology and biotechnology has motivated the development of systematic approaches to their discovery and characterization. Here we present a methodology for reliable detection of genomic ribozymes that centers on pipelined structure-based searches, utilizing two versatile algorithms for structure prediction. RNArobo is a prototype structure-based search package that enables a single search to return all sequences matching a designated motif descriptor, taking into account the possibility of single nucleotide insertions within base-paired regions. These outputs are then filtered through a structure prediction algorithm based on free energy minimization in order to maximize the proportion of catalytically active RNA motifs. This pipeline provides a fast approach to uncovering new catalytic RNAs with known secondary structures and verifying their activity in vitro.

Key words

Ribozymes Pseudoknots RNABOB RNArobo RNAfold 



The authors gratefully acknowledge support from VEGA (1/0210/10) to T.V. at the Faculty of Mathematics, Physics and Informatics, Comenius University; and the Pew Charitable Trusts, the NIH (GM094929-01), and the University of California–Irvine to A.L.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Randi M. Jimenez
    • 1
  • Ladislav Rampášek
    • 2
  • Broňa Brejová
    • 3
  • Tomáš Vinař
    • 2
  • Andrej Lupták
    • 1
  1. 1.Department of Pharmaceutical SciencesUniversity of CaliforniaIrvineUSA
  2. 2.Faculty of Mathematics, Physics and InformaticsComenius UniversityBratislavaUSA
  3. 3.Natural Sciences IIUniversity of CaliforniaIrvineUSA

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