{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:18:12Z","timestamp":1764688692496},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"10","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment. The predictions are therefore highly sensitive to alignment errors or regions of alignment uncertainty. Alternatively, statistical alignment methods provide a framework for performing phylogenetic analyses by examining a distribution of alignments.<\/jats:p>\n               <jats:p>Results: We developed a novel algorithm for predicting functional elements by combining statistical alignment and phylogenetic footprinting (SAPF). SAPF simultaneously performs both alignment and annotation by combining phylogenetic footprinting techniques with an hidden Markov model (HMM) transducer-based multiple alignment model, and can analyze sequence data from multiple sequences. We assessed SAPF's predictive performance on two simulated datasets and three well-annotated cis-regulatory modules from newly sequenced Drosophila genomes. The results demonstrate that removing the traditional dependence on a single alignment can significantly augment the predictive performance, especially when there is uncertainty in the alignment of functional regions.<\/jats:p>\n               <jats:p>Availability: SAPF is freely available to download online at http:\/\/www.stats.ox.ac.uk\/~satija\/SAPF\/<\/jats:p>\n               <jats:p>Contact: \u00a0satija@stats.ox.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn104","type":"journal-article","created":{"date-parts":[[2008,3,20]],"date-time":"2008-03-20T00:25:10Z","timestamp":1205972710000},"page":"1236-1242","source":"Crossref","is-referenced-by-count":26,"title":["Combining statistical alignment and phylogenetic footprinting to detect regulatory elements"],"prefix":"10.1093","volume":"24","author":[{"given":"Rahul","family":"Satija","sequence":"first","affiliation":[{"name":"1 Department of Statistics, Oxford University, Oxford, UK and 2Department of Mathematics, Univeristy of California, Berkeley, CA, USA"}]},{"given":"Lior","family":"Pachter","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Oxford University, Oxford, UK and 2Department of Mathematics, Univeristy of California, Berkeley, CA, USA"}]},{"given":"Jotun","family":"Hein","sequence":"additional","affiliation":[{"name":"1 Department of Statistics, Oxford University, Oxford, UK and 2Department of Mathematics, Univeristy of California, Berkeley, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2008,3,18]]},"reference":[{"key":"2023020210051114700_B1","doi-asserted-by":"crossref","first-page":"2185","DOI":"10.1126\/science.287.5461.2185","article-title":"The genome sequence of Drosophila melanogaster","volume":"287","author":"Adams","year":"2000","journal-title":"Science"},{"key":"2023020210051114700_B2","doi-asserted-by":"crossref","first-page":"1747","DOI":"10.1093\/bioinformatics\/bti173","article-title":"Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster","volume":"21","author":"Bergman","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020210051114700_B3","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.1126\/science.1081331","article-title":"Phylogenetic shadowing of primate sequences to find functional regions of the human genome","volume":"299","author":"Boffelli","year":"2003","journal-title":"Science"},{"key":"2023020210051114700_B4","doi-asserted-by":"crossref","first-page":"3258","DOI":"10.1093\/bioinformatics\/btm402","article-title":"Transducers: an emerging probabilistic framework for modeling indels on trees","volume":"23","author":"Bradley","year":"2007","journal-title":"Bioinformatics"},{"key":"2023020210051114700_B5","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1126\/science.1084337","article-title":"Finding functional features in Saccharomyces genomes by phylogenetic footprinting","volume":"301","author":"Cliften","year":"2003","journal-title":"Science"},{"key":"2023020210051114700_B6","doi-asserted-by":"crossref","first-page":"e73","DOI":"10.1371\/journal.pcbi.0020073","article-title":"Parametric alignment of Drosophila genomes","volume":"2","author":"Dewey","year":"2006","journal-title":"PLoS Computat. 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