Comparative Genomics pp 503-525

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

Prediction of Structural Noncoding RNAs With RNAz

  • Stefan Washietl

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 

Copyright information

© Humana Press Inc. 2007

Authors and Affiliations

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

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