Format

Send to

Choose Destination
Genome Res. 2002 May;12(5):739-48.

Discovery of regulatory elements by a computational method for phylogenetic footprinting.

Author information

1
Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195-2350, USA.

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.

PMID:
11997340
PMCID:
PMC186562
DOI:
10.1101/gr.6902
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center