Journal Article

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

Parvez Anandam, Elfar Torarinsson and Walter L. Ruzzo

in Bioinformatics

Volume 25, issue 5, pages 668-669
Published in print March 2009 | ISSN: 1367-4803
Published online January 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp006
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies

More Like This

Show all results sharing this subject:

  • Bioinformatics and Computational Biology

GO

Show Summary Details

Preview

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@u.washington.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1640 words. 

Subjects: Bioinformatics and Computational Biology

Full text: subscription required

How to subscribe Recommend to my Librarian

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.