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Bioinformatics Advance Access originally published online on January 9, 2009
Bioinformatics 2009 25(5):668-669; doi:10.1093/bioinformatics/btp006
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

Parvez Anandam 1,*, Elfar Torarinsson 2 and Walter L. Ruzzo 1,3

1Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195-2350, USA, 2Department of Natural Sciences, Faculty of Life Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark and 3Department of Genome Sciences, University of Washington, Seattle, WA 98195-2350, USA

*To whom correspondence should be addressed.


  Abstract

Summary: 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.

Availability: The Multiperm GNU Cb++ source code is available at http://www.anandam.name/multiperm

Contact: anandam{at}u.washington.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on November 3, 2008; revised on December 2, 2008; accepted on December 30, 2008

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