PPT Slide
Large parts of known E. coli regulons can be predicted in this manner (i.e. ArgR, PurR)
We used 343 groups obtained in this manner in each of 17 organisms to search for motifs.
Using AlignACE, known E. coli motifs can be found using these groups of genes (i.e. ArgR, PurR)
The ArgR and PurR motifs are in the top 10 out of 50,000 motifs when all motifs found in this manner are ranked by specificity score and palindromicity.