{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T03:44:17Z","timestamp":1773200657920,"version":"3.50.1"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation : With over 9000 unique users recorded in the first half of 2013, MEME is one of the most popular motif-finding tools available. Reliable estimates of the statistical significance of motifs can greatly increase the usefulness of any motif finder. By analogy, it is difficult to imagine evaluating a BLAST result without its accompanying E -value. Currently MEME evaluates its EM-generated candidate motifs using an extension of BLAST\u2019s E -value to the motif-finding context. Although we previously indicated the drawbacks of MEME\u2019s current significance evaluation, we did not offer a practical substitute suited for its needs, especially because MEME also relies on the E -value internally to rank competing candidate motifs.<\/jats:p><jats:p>Results : Here we offer a two-tiered significance analysis that can replace the E -value in selecting the best candidate motif and in evaluating its overall statistical significance. We show that our new approach could substantially improve MEME\u2019s motif-finding performance and would also provide the user with a reliable significance analysis. In addition, for large input sets, our new approach is in fact faster than the currently implemented E -value analysis.<\/jats:p><jats:p>Contact : uri.keich@sydney.edu.au or emi.tanaka@sydney.edu.au<\/jats:p><jats:p>Supplementary information : Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu163","type":"journal-article","created":{"date-parts":[[2014,3,25]],"date-time":"2014-03-25T04:53:46Z","timestamp":1395723226000},"page":"1965-1973","source":"Crossref","is-referenced-by-count":23,"title":["Improving MEME via a two-tiered significance analysis"],"prefix":"10.1093","volume":"30","author":[{"given":"Emi","family":"Tanaka","sequence":"first","affiliation":[{"name":"1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia"},{"name":"1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia"}]},{"given":"Timothy L.","family":"Bailey","sequence":"additional","affiliation":[{"name":"1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia"}]},{"given":"Uri","family":"Keich","sequence":"additional","affiliation":[{"name":"1 School of Mathematics and Statistics, University of Sydney, Sydney 2006, 2 School of Mathematics and Applied Statistics, University of Wollongong, Wollongong 2522, New South Wales and 3 Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia"}]}],"member":"286","published-online":{"date-parts":[[2014,3,24]]},"reference":[{"key":"2023012711244990100_btu163-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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