Discovery of regulatory elements by a computational method for phylogenetic footprinting.
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.
Blanchette
Mathieu
M
Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195-2350, USA.
Tompa
Martin
M
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods*; D018983:DNA Footprinting / Q000379:methods*; D029941:Fish Proteins; D016762:Genes, fos / Q000235:genetics; D016259:Genes, myc / Q000235:genetics; D013006:Growth Hormone / Q000235:genetics; D006801:Humans; D007328:Insulin / Q000235:genetics; D007377:Interleukin-3 / Q000235:genetics; D007438:Introns / Q000235:genetics; D008668:Metallothionein / Q000235:genetics; D005810:Multigene Family / Q000235:genetics; D010802:Phylogeny; D011401:Promoter Regions, Genetic / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*
D029941:Fish Proteins; D007328:Insulin; D007377:Interleukin-3; C074134:growth hormone type I, Salmo salar; D013006:Growth Hormone; D008668:Metallothionein