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

ABSTRACT: 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.

SUBMITTER: Wang G

PROVIDER: S-EPMC1779545 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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

Wang Guandong G Zhang Weixiong W

Genome biology 20060101 6

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 co ...[more]

PMID: 16787547

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