Prediction of Structural Noncoding RNAs With RNAz

  • Stefan Washietl
Part of the Methods in Molecular Biology™ book series (MIMB, volume 395)

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.

Key Words

Noncoding RNA gene finding conserved RNA secondary structure RNA structure prediction 

Notes

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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Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

  • Stefan Washietl
    • 1
  1. 1.Department of Theoretical ChemistryUniversity of ViennaViennaAustria

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