title: Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.
abstract: CONCLUSIONS
  Assessing the statistical significance of structured RNA predicted from multiple sequence alignments relies on the existence of a good null model. We present here a random shuffling algorithm, Multiperm, that preserves not only the gap and local conservation structure in alignments of arbitrarily many sequences, but also the approximate dinucleotide frequencies. No shuffling algorithm that simultaneously preserves these three characteristics of a multiple (beyond pairwise) alignment has been available to date. As one benchmark, we show that it produces shuffled exonic sequences having folding free energy closer to native sequences than shuffled alignments that do not preserve dinucleotide frequencies.
  
  
  BACKGROUND
  The Multiperm GNU Cb++ source code is available at http://www.anandam.name/multiperm
authors.affiliation: Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA. anandam@u.washington.edu
authors.forename: Parvez
authors.initials: P
authors.lastname: Anandam
authors.forename: Elfar
authors.initials: E
authors.lastname: Torarinsson
authors.forename: Walter L
authors.initials: WL
authors.lastname: Ruzzo
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D009711:Nucleotides / Q000032:analysis; D012313:RNA / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA; D013816:Thermodynamics
chemical_list: D009711:Nucleotides; D012313:RNA