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The method incorporates the phylogenies of the species under consideration and takes into account the position specific variation of transcription factor binding sites. Using our framework we assessed the suitability of alignments of genomic sequences from commonly used species as substrates for comparative genomic approaches to regulatory motif finding. We then applied this technique to <jats:italic>Saccharomyces cerevisiae<\/jats:italic> and related species by examining all possible six base pair DNA sequences (hexamers) and identifying sequences that are conserved in a significant number of promoters. By combining similar conserved hexamers we reconstructed known cis-regulatory motifs and made predictions of previously unidentified motifs. We tested one prediction experimentally, finding it to be a regulatory element involved in the transcriptional response to glucose.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusion<\/jats:title>\n            <jats:p>The experimental validation of a regulatory element prediction missed by other large-scale motif finding studies demonstrates that our approach is a useful addition to the current suite of tools for finding regulatory motifs.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-7-266","type":"journal-article","created":{"date-parts":[[2006,5,23]],"date-time":"2006-05-23T06:45:40Z","timestamp":1148366740000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Phylogeny based discovery of regulatory elements"],"prefix":"10.1186","volume":"7","author":[{"given":"Jason","family":"Gertz","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Justin C","family":"Fay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barak A","family":"Cohen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2006,5,22]]},"reference":[{"key":"1005_CR1","doi-asserted-by":"publisher","first-page":"S140","DOI":"10.1093\/bioinformatics\/17.suppl_1.S140","volume":"17 Suppl 1","author":"I Korf","year":"2001","unstructured":"Korf I, Flicek P, Duan D, Brent MR: Integrating genomic homology into gene structure prediction. 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