Prediction of structural noncoding RNAs with RNAz.
The function of many noncoding RNAs (ncRNAs) depend on a defined secondary structure. RNAz detects evolutionarily conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments and, thus, efficiently filters for candidate ncRNAs. In this chapter, we provide a step-by-step guide on how to use RNAz. Starting with basic concepts, we also cover advanced analysis techniques and, as an example for a large scale application, demonstrate a complete screen of the Saccharomyces cerevisiae genome.
Washietl
Stefan
S
Department of Theoretical Chemistry, University of Vienna.
D001483:Base Sequence; D009690:Nucleic Acid Conformation; D022661:RNA, Untranslated / Q000737:chemistry*; D012689:Sequence Homology, Nucleic Acid; D013816:Thermodynamics
D022661:RNA, Untranslated