Figure 6

κB sites with greater HMM occupancy probability are conserved better. Each curve represents the kernel-smoothing density estimate of the evolutionary conservation scores of a set of κB sites. Each set consists of κB sites predicted by OHMM to have occupancy probability above a threshold shown in the legend. The "random" set consists of 1000 10-tuples randomly selected from the human promoters. Conservation scores of κB sites predicted by OHMM are higher than those of the random sequences. Moreover, κB sites with higher HMM occupancy probability have higher conservation scores. Conservation scores and kernel-smoothing density estimates were calculated as described in the Methods section.