EDGI: Enhancer Detection using only Genomic Information
EDGI integrates a traditional motif-discovery algorithm SPLASH with a novel local permutation-clustering algorithm PromoClust in order to identify large regulatory elements (e.g. enhancers) as evolutionarily conserved, order-independent clusters of short conserved motifs. EDGI relies on the evolutionary conservation of the binding sites for regulating transcription factors, without requiring knowledge of these transcription factors or their binding sites.
Sosinsky A, Honig B, Mann RS, Califano A. Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting. Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6305-10.
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