Comparative Genomics pp 503-525
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.