Carmack, CS, McCue, LA, Newberg, LA and Lawrence, CE (2007) PhyloScan: identification of transcription factor binding sites using cross-species evidence. Algorithms Mol Biol 2:1
When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for additional sites. However, few statistically significant sites are revealed when a transcription factor binding site motif model is used to scan a genome-scale database.
You can scan for transcription factor binding sites in E. coli using the associated PhyloScan web server.
Useful Materials and Methods
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