Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting Export

@article{citeulike:489958, abstract = {Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.}, author = {Blanchette, Mathieu and Tompa, Martin}, citeulike-article-id = {489958}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.6902}, citeulike-linkout-1 = {http://genome.cshlp.org/content/12/5/739.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/12/5/739.full.pdf}, citeulike-linkout-3 = {http://www.genome.org/cgi/content/abstract/12/5/739}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/11997340}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=11997340}, day = {1}, doi = {10.1101/gr.6902}, journal = {Genome Res.}, keywords = {ab\_initio, binding\_site, conservation, method, prediction}, month = {May}, number = {5}, pages = {739--748}, posted-at = {2007-11-01 00:41:11}, priority = {0}, title = {Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting}, url = {http://dx.doi.org/10.1101/gr.6902}, volume = {12}, year = {2002} }

TY - JOUR ID - citeulike:489958 L3 - citeulike-article-id:489958 N2 - Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known. IS - 5 JF - Genome Res. EP - 748 TI - Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting VL - 12 SP - 739 KW - ab_initio KW - binding_site KW - conservation KW - method KW - prediction AU - Blanchette, Mathieu AU - Tompa, Martin PY - 2002/05/01/ UR - http://dx.doi.org/10.1101/gr.6902 ER -