Comparative ncRNA Gene and Structure Prediction Using Foldalign and FoldalignM

Jakob Havgaard1, Simranjeet Kaur1, Jan Gorodkin1

1 Center for Non‐Coding RNA in Technology and Health, Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.11
DOI:  10.1002/0471250953.bi1211s39
Online Posting Date:  September, 2012
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Abstract

This unit describes how to use Foldalign and FoldalignM to make structural alignments of non‐protein‐coding‐RNA (ncRNA). These tools can be used to find new ncRNAs, to find the structure of novel ncRNAs, and to improve alignments for known ncRNAs. Curr. Protoc. Bioinform. 39:12.11.1‐12.11.15. © 2012 by John Wiley & Sons, Inc.

Keywords: ncRNA; RNA structural alignment; RNA structure prediction; RNA multiple sequence alignment; ncRNA gene finding; non‐coding RNA

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Searching for New RNA Structures Using Foldalign
  • Basic Protocol 2: Pairwise Global Structural Alignment Using Foldalign
  • Alternate Protocol 1: Pairwise Local Structural Alignment Using the Foldalign Web Server
  • Basic Protocol 3: Multiple Alignment Using FoldalignM and the Foldalign Scoring Method
  • Alternate Protocol 2: Multiple Alignment Using FoldalignM and the McCaskill Scoring Method
  • Basic Protocol 4: AlignToStructure
  • Support Protocol 1: Installing Foldalign
  • Support Protocol 2: Installing FoldalignM
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

   Gardner, P., Wilm, A., and Washietl, S. 2005. A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res. 33:2433‐2439.
   Gorodkin, J., Heyer, L., and Stormo, G. 1997a. Finding common sequence and structure motifs in a set of RNA sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 5:120‐123.
   Gorodkin, J., Heyer, L., and Stormo, G. 1997b. Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Res. 25:3724‐3732.
   Gorodkin, J., Lyngso, R., and Stormo, G. 2001a. A mini‐greedy algorithm for faster structural RNA stem‐loop search. Genome Inform. Ser. Workshop Genome Inform. 12:184‐193.
   Gorodkin, J., Stricklin, S., and Stormo, G. 2001b. Discovering common stem‐loop motifs in unaligned RNA sequences. Nucleic Acids Res. 29:2135‐2144.
   Havgaard, J., Lyngso, R., Stormo, G., and Gorodkin, J. 2005a. Pairwise local structural alignment of RNA sequences with sequence similarity less than 40. Bioinformatics 21:1815‐1824.
   Havgaard, J., Lyngsø, R., and Gorodkin, J. 2005b. The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res. 33:W650‐W653.
   Havgaard, J., Torarinsson, E., and Gorodkin, J. 2007. Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol. 3:1896‐1908.
   Klein, R. and Eddy, S. 2003. RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinformatics 4:44.
   Mathews, D., Sabina, J., Zuker, M., and Turner, D. 1999. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288:911‐940.
   McCaskill, J. 1990. The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29:1105‐1119.
   Sankoff, D. 1985. Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math. 45:810‐825.
   Torarinsson, E., Sawera, M., Havgaard, J., Fredholm, M., and Gorodkin, J. 2006. Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res. 16:885‐889.
   Torarinsson, E., Havgaard, J., and Gorodkin, J. 2007. Multiple structural alignment and clustering of RNA sequences. Bioinformatics 23:926‐932.
Key References
   Havgaard et al., 2007. See above.
  Describes the latest implementation of the Foldalign algorithm.
   Havgaard et al., 2005a. See above.
  A more detailed description of the energy‐ and substitution‐ models used by Foldalign.
   Havgaard et al., 2005b. See above.
  Describes the Foldalign Web server.
   Torarinsson et al., 2006. See above.
  A large‐scale search for novel ncRNA structures in human and mouse using Foldalign.
   Torarinsson et al., 2007. See above.
  Describes the FoldalignM algorithm.
   Torarinsson, E. and Lindgreen, S. 2008. WAR: Webserver for aligning structural RNAs. Nucleic Acids Res. 36:W79‐W84.
  Describes the Web server for aligning structural RNAs, which includes FoldalignM as well as other methods.
Internet Resources
  http://foldalign.ku.dk
  The Foldalign Web site, the Foldalign Web server, and extra documentation, as well as the source code for Foldalign and FoldalignM can be found here.
   http://genome.ku.dk/resources/war/
  The Web server for aligning structural RNAs, which among many other methods includes FoldalignM.
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