{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,10,8]],"date-time":"2024-10-08T04:15:02Z","timestamp":1728360902005},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2004,9,15]],"date-time":"2004-09-15T00:00:00Z","timestamp":1095206400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"},{"start":{"date-parts":[[2004,9,15]],"date-time":"2004-09-15T00:00:00Z","timestamp":1095206400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                        <jats:title>Background<\/jats:title>\n                        <jats:p>In addition to known protein-coding genes, large amounts of apparently non-coding sequence are conserved between the human and mouse genomes. It seems reasonable to assume that these conserved regions are more likely to contain functional elements than less-conserved portions of the genome.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Methods<\/jats:title>\n                        <jats:p>Here we used a motif-oriented machine learning method based on the Relevance Vector Machine algorithm to extract the strongest signal from a set of non-coding conserved sequences.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Results<\/jats:title>\n                        <jats:p>We successfully fitted models to reflect the non-coding sequences, and showed that the results were quite consistent for repeated training runs. Using the learned models to scan genomic sequence, we found that they often made predictions close to the start of annotated genes. We compared this method with other published promoter-prediction systems, and showed that the set of promoters which are detected by this method is substantially similar to that detected by existing methods.<\/jats:p>\n                     <\/jats:sec><jats:sec>\n                        <jats:title>Conclusions<\/jats:title>\n                        <jats:p>The results presented here indicate that the promoter signal is the strongest single motif-based signal in the non-coding functional fraction of the genome. They also lend support to the belief that there exists a substantial subset of promoter regions which share several common features including, but not restricted to, a relative abundance of CpG dinucleotides. This subset is detectable by a variety of distinct computational methods.<\/jats:p>\n                     <\/jats:sec>","DOI":"10.1186\/1471-2105-5-131","type":"journal-article","created":{"date-parts":[[2004,9,21]],"date-time":"2004-09-21T06:23:48Z","timestamp":1095747828000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["What can we learn from noncoding regions of similarity between genomes?"],"prefix":"10.1186","volume":"5","author":[{"given":"Thomas A","family":"Down","sequence":"first","affiliation":[]},{"given":"Tim JP","family":"Hubbard","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2004,9,15]]},"reference":[{"key":"247_CR1","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"The Genome International Sequencing Consortium","year":"2001","unstructured":"The Genome International Sequencing Consortium: Initial sequencing and analysis of the human genome.\n                           Nature 2001, 409: 860\u2013921. 10.1038\/35057062","journal-title":"Nature"},{"key":"247_CR2","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/nature01262","volume":"420","author":"The Mouse Genome Sequencing Consortium","year":"2002","unstructured":"The Mouse Genome Sequencing Consortium: Initial sequencing and comparative analysis of the mouse genome.\n                           Nature 2002, 420: 520\u2013562. 10.1038\/nature01262","journal-title":"Nature"},{"key":"247_CR3","doi-asserted-by":"publisher","first-page":"R1","DOI":"10.1186\/gb-2002-4-1-r1","volume":"4","author":"Z Xuan","year":"2002","unstructured":"Xuan Z, Wang J, Zhang M: Computational comparison of two mouse draft genomes and the human golden path.\n                           Genome Biology 2002, 4: R1. 10.1186\/gb-2002-4-1-r1","journal-title":"Genome 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Detection and Location of Transcription Start Sites in Mammalian Genomic DNA.\n                           Genome Res. 2002, 12: 652\u2013658. 10.1101\/gr.216102","journal-title":"Genome Res"},{"key":"247_CR7","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1016\/0022-2836(90)90223-9","volume":"212","author":"P Bucher","year":"1990","unstructured":"Bucher P: Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences.\n                           Journal of Molecular Biology 1990, 212: 563\u2013578.","journal-title":"Journal of Molecular Biology"},{"key":"247_CR8","doi-asserted-by":"publisher","first-page":"805","DOI":"10.1038\/nature02055","volume":"425","author":"A Mungall","year":"2003","unstructured":"Mungall A, Palmer S, Sims S, Edwards C, Ashurst J, Wilming L, Jones M, Horton R, Hunt S, Scott C, Gilbert J, Clamp M, Bethel G, Milne S, Ainscough R, Almeida J, Ambrose K, Andrews T, Ashwell R, Babbage A, Bagguley C, Bailey J, Banerjee R, Barker D, Barlow K, Bates K, Beare D, Beasley H, Beasley O, Bird C, Blakey S, Bray-Allen S, Brook J, Brown A, Brown J, Burford D, Burrill W, Burton J, Carder C, Carter N, Chapman J, Clark S, Clark G, Glee C, Clegg S, Cobley V, Collier R, Collins J, Colman L, Corby N, Coville G, Culley K, Dhami P, Davies J, Dunn M, Earthrowl M, Ellington A, Evans K, Faulkner L, Francis M, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori M, Gilby L, Gillson C, Glithero R, Grafham D, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls K, Hammond S, Harley J, Hart E, Heath P, Heathcott R, Holmes S, Howden P, Howe K, Howell G, Huckle E, Humphray S, Humphries M, Hunt A, Johnson C, Joy A, Kay M, Keenan S, Kimberley A, King A, Laird G, Langford C, Lawlor S, Leongamornlert D, Leversha M, Lloyd C, Lloyd D, Loveland J, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen G, Matthews L, McCann O, McLaren S, McLay K, McMurray A, Moore M, Mullikin J, Niblett D, 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A, Freeh K, Quandt K, Schneider R, Grote K, Frisch M, Gailus-Durner V, Seidel A, Brack-Werner R, Werner T: First pass annotation of promoters on human chromosome 22.\n                           Genome Res. 2001, 11: 333\u2013340. 10.1101\/gr.154601","journal-title":"Genome Res"},{"key":"247_CR16","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1093\/nar\/30.7.e30","volume":"30","author":"S Cross","year":"2002","unstructured":"Cross S, Bird A: The Ensembl genome database project.\n                           Nucleic Acids Res. 2002, 30: 30\u201331. 10.1093\/nar\/30.7.e30","journal-title":"Nucleic Acids Res"},{"key":"247_CR17","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/nar\/28.1.302","volume":"28","author":"R Perier","year":"2000","unstructured":"Perier R, Praz V, Junier T, Bonnard C, Bucher P: The Eukaryotic Promoter Database (EPD).\n                           Nucleic Acids Res. 2000, 28: 307\u2013309. 10.1093\/nar\/28.1.302","journal-title":"Nucleic Acids 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December 2003","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 September 2004","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 September 2004","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"131"}}