Discovering Motif Interactions in Gene Promoter Regions
We seek to understand the rules governing the organization of cis-regulatory elements in promoter regions of saccharomyces cerevisiae(yeast). Starting with a library of known motifs, we construct a Hidden Markov Model where states correspond either to positions within different motifs or to background states. By learning the transition probabilities of this HMM we uncover preferences in ordering and orientations between cis-regulatory elements.