Details

Autor(en) / Beteiligte

• Jimenez, Randi M
• Rampášek, Ladislav
• Brejová, Broňa
• Vinař, Tomáš
• Lupták, Andrej

Titel

Discovery of RNA motifs using a computational pipeline that allows insertions in paired regions and filtering of candidate sequences

Ist Teil von

• Methods in molecular biology (Clifton, N.J.), 2012, Vol.848, p.145

Ort / Verlag

United States

Erscheinungsjahr

2012

Quelle

MEDLINE

Beschreibungen/Notizen

• 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.