Summary
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.
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Acknowledgments
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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Washietl, S. (2007). Prediction of Structural Noncoding RNAs With RNAz. In: Bergman, N.H. (eds) Comparative Genomics. Methods in Molecular Biology™, vol 395. Humana Press. https://doi.org/10.1007/978-1-59745-514-5_32
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DOI: https://doi.org/10.1007/978-1-59745-514-5_32
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