Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting.

ABSTRACT: The functional annotation of the nonprotein-coding DNA of eukaryotic genomes is a problem of central importance. Phylogenetic footprinting methods, which attempt to identify functional regulatory regions by comparing orthologous genomic sequences of evolutionarily related species, have shown promising results. The main advantage of this class of approaches is that they do not require any knowledge of the regulating transcription factors. Here we describe a method called Enhancer Detection using only Genomic Information (EDGI), which integrates a traditional motif-discovery algorithm with a local permutation-clustering algorithm. Together, they can identify large regulatory elements (e.g., enhancers) as evolutionarily conserved order-independent clusters of short conserved motifs. We show t

SUBMITTER: Sosinsky A 

PROVIDER: S-EPMC1851073 | biostudies-literature | 2007 Apr

REPOSITORIES: biostudies-literature