TitleMultiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.
Publication TypeJournal Article
Year of Publication2009
AuthorsAnandam P, Torarinsson E, Ruzzo WL
JournalBioinformatics (Oxford, England)
Date or Month Published2009 Mar 1
KeywordsAlgorithms, Computational Biology, Nucleotides, RNA, Sequence Alignment, Sequence Analysis, RNA, Thermodynamics

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


http://www.ncbi.nlm.nih.gov/pubmed/19136551?dopt=Abstract Abstract

Alternate JournalBioinformatics
Citation Key1868
PubMed ID19136551