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A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements

Guandong Wang1 and Weixiong Zhang12*

Author Affiliations

1 Department of Computer Science and Engineering, Washington University, St. Louis, MO 63130, USA

2 Department of Genetics, Washington University, St. Louis, MO 63130, USA

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Genome Biology 2006, 7:R49  doi:10.1186/gb-2006-7-6-r49

Published: 20 June 2006


The comprehensive identification of cis-regulatory elements on a genome scale is a challenging problem. We develop a novel, steganalysis-based approach for genome-wide motif finding, called WordSpy, by viewing regulatory regions as a stegoscript with cis-elements embedded in 'background' sequences. We apply WordSpy to the promoters of cell-cycle-related genes of Saccharomyces cerevisiae and Arabidopsis thaliana, identifying all known cell-cycle motifs with high ranking. WordSpy can discover a complete set of cis-elements and facilitate the systematic study of regulatory networks.