Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting

by: Mathieu Blanchette, Martin Tompa

Genome Res., Vol. 12, No. 5. (1 May 2002), pp. 739-748.

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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.

@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}, 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} }

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TY - JOUR ID - citeulike:489958 L3 - citeulike-article-id:489958 TI - Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting JF - Genome Res. VL - 12 IS - 5 SP - 739 EP - 748 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. 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 -

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