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.
journal_name
Genome Resjournal_title
Genome researchauthors
Blanchette M,Tompa Mdoi
10.1101/gr.6902subject
Has Abstractpub_date
2002-05-01 00:00:00pages
739-48issue
5eissn
1088-9051issn
1549-5469journal_volume
12pub_type
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