Outline
Using AlignACE, searched for DNA regulatory motifs in 17 genomes using potentially coregulated sets of genes obtained by 3 different methods
obtained > 100,000 motifs from 14,863 AlignACE runs (2 months of CPU time on 8 400 MHz processors)
Ranked motifs according to specificity score, MAP score, and palindromicity
Examined conservation of known E. coli motifs in other organisms