{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T20:47:48Z","timestamp":1770410868061,"version":"3.49.0"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: The Multiperm GNU Cb++ source code is available at http:\/\/www.anandam.name\/multiperm<\/jats:p>\n               <jats:p>Contact: \u00a0anandam@u.washington.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp006","type":"journal-article","created":{"date-parts":[[2009,1,10]],"date-time":"2009-01-10T01:34:33Z","timestamp":1231551273000},"page":"668-669","source":"Crossref","is-referenced-by-count":23,"title":["Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies"],"prefix":"10.1093","volume":"25","author":[{"given":"Parvez","family":"Anandam","sequence":"first","affiliation":[{"name":"1 Department 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"}]},{"given":"Elfar","family":"Torarinsson","sequence":"additional","affiliation":[{"name":"1 Department 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"}]},{"given":"Walter L.","family":"Ruzzo","sequence":"additional","affiliation":[{"name":"1 Department 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"},{"name":"1 Department 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"}]}],"member":"286","published-online":{"date-parts":[[2009,1,9]]},"reference":[{"key":"2023013110114103700_B1","first-page":"526","article-title":"Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage","volume":"2","author":"Altschul","year":"1985","journal-title":"Mol. 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