Medicine and Health Sciences Commons^™

Scope: A Web Server For Practical De Novo Motif Discovery, Jonathan M. Carlson, Arijit Chakravarty, Charles E. Deziel, Robert H. Gross

Dartmouth Scholarship

SCOPE is a novel parameter-free method for the de novoidentification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a …