Randi M. Jimenez, Ladislav Rampášek, Broňa Brejová, Tomáš Vinař, Andrej Lupták. Discovery of RNA Motifs Using a Computational Pipeline that Allows Insertions in Paired Regions and Filtering of Candidate Sequences . In Jörg S. Hartig, ed., Ribozymes: Methods and Protocols, 848 volume of Methods in Molecular Biology, chapter 10, pp. 145-158, 2012. Springer.

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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.