Identifying Dyads and their conservation in Drosphila.

Core promoter regions in Drosophila are enriched with binding sites like TATA, Inr, DPE, MTE, etc. They have very strict spacing between each other in promoters where they occur together. For example, in Drosophila melanogaster TATA-Inr has a spacing of 25-30 bp. Our aim in this work is to identify all such pair of motifs having strict positional constraint in the core promoters of all Drosophila species. We discover how these motifs and the spacing between them evolve within Drosophila species. For this we analyze 700 bp upstream and 300 bp downstream of TSS in D. melanogaster and the corresponding orthologous region in other Drosophila species. For each species, this 1000 bp region is searched for statistically over-represented compound words of the form W1N{L}W2, where L is the spacing between words W1 and W2. These compound words are systematically clustered for further analysis.