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.
Key WordsNoncoding RNA gene finding conserved RNA secondary structure RNA structure prediction
The author thanks Ivo L. Hofacker and Peter F. Stadler for helpful discussions and assistance during the development of RNAz. This work was supported by Austrian GEN-AU project “noncoding RNA.”
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