RT Journal
A1 Blanchette, Mathieu
A1 Tompa, Martin
T1 Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting
JF Genome Research 
JO Genome Research 
YR 2002 
FD May 01 
VO 12 
IS 5 
SP 739 
OP 748 
DO 10.1101/gr.6902 
UL http://genome.cshlp.org/content/12/5/739.abstract 
AB 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.