Identifying Structural Noncoding RNAs Using RNAz

Stefan Washietl1, Ivo L. Hofacker1

1 University of Vienna, Vienna, Austria
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.7
DOI:  10.1002/0471250953.bi1207s19
Online Posting Date:  September, 2007
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Abstract

The functions of many noncoding RNAs and cis‐acting regulatory elements of mRNAs depend on a defined RNA secondary structure. RNAz predicts such functional RNA structures on the basis of thermodynamic stability and evolutionary conservation of homologous sequences. It can be used to efficiently filter multiple alignments for noncoding RNA candidates in genomic screens. Curr. Protoc. Bioinform. 19:12.7.1‐12.7.18. © 2007 by John Wiley & Sons, Inc.

Keywords: RNA structure; noncoding RNA; structure conservation; comparative genomics; gene prediction

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Using RNAz to Analyze a Simple Alignment
  • Basic Protocol 2: Analyzing More Complex Alignments
  • Alternate Protocol 1: Using alifoldz.pl
  • Basic Protocol 3: Using RNAz to Perform a Large‐Scale Genomic Screen
  • Alternate Protocol 2: Using the RNAz Web Server
  • Support Protocol 1: Installing Necessary Software
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Athanasius F. Bompfünewerer Consortium, Backofen, R., Bernhart, S.H., Flamm, C., Fried, C., Fritzsch, G., Hackermüller, J., Hertel, J., Hofacker, I.L., Missal, K., Mosig, A., Prohaska, S.J., Rose, D., Stadler, P.F., Tanzer, A., Washietl, S., and Will, S. 2007. RNAs everywhere: Genome‐wide annotation of structured RNAs. J. Exp. Zool. B Mol. Dev. Evol. 308:1‐25.
   Bompfünewerer, A., Flamm, C., Fried, C., Fritzsch, G., Hofacker, I., Lehmann, J., Missal, K., Mosig, A., Müller, B., Prohaska, S., Stadler, B., Stadler, P., Tanzer, A., Washietl, S., and Witwer, C. 2005. Evolutionary patterns of non‐coding RNAs. Theory Biosci. 123:301‐369.
   Frith, M.C., Pheasant, M., and Mattick, J.S. 2005. The amazing complexity of the human transcriptome. Eur. J. Hum. Genet. 13:894‐897.
   Griffiths‐Jones, S., Moxon, S., Marshall, M., Khanna, A., Eddy, S.R., and Bateman, A. 2005. Rfam: Annotating non‐coding RNAs in complete genomes. Nucl. Acids Res. 33:D121‐D124.
   Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, S., Tacker, M., and Schuster, P. 1994. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125:167‐188.
   Hofacker, I.L., Fekete, M., and Stadler, P.F. 2002. Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319:1059‐1066.
   Martens, J.A., Laprade, L., and Winston, F. 2004. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene. Nature 429:571‐574.
   Washietl, S. and Hofacker, I.L. 2004. Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics. J. Mol. Biol. 342:19‐30.
   Washietl, S., Hofacker, I.L., and Stadler, P.F. 2005. Fast and reliable prediction of noncoding RNAs. Proc. Natl. Acad. Sci. U.S.A. 102:2454‐2459.
Key References
   Hofacker et al., 2002. See above.
  This paper describes the basic algorithm to predict a consensus structure for aligned sequences. All programs described in this unit build upon this algorithm.
   Washietl and Hofacker 2004. See above.
  This paper introduces the alifoldz.pl algorithm and demonstrates that only comparative analysis has enough statistical power to predict functional structures with reasonable accuracy.
   Washietl et al., 2005. See above.
  This paper provides the reader with detailed description of the RNAz algorithm.
Internet Resources
  http://www.tbi.univie.ac.at/∼wash/RNAz/
  Download the latest version ofRNAz; read online manuals.
  http://rna.tbi.univie.ac.at/RNAz
  RNAz Web server.
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