Comparison of Promoter Sequences Based on Inter Motif Distance

Abstract

Understanding how the regulation of gene networks is orchestrated is an important challenge for characterizing complex biological processes. The DNA sequences that comprise promoters do not provide much direct information about regulation. A substantial part of the regulation results from the interaction of transcription factors (TFs) with specific cis regulatory DNA sequences. These regulatory sequences are organized in a modular fashion, with each module (enhancer) containing one or more binding sites for a specific combination of TFs. In the present work, the authors have proposed to investigate the inter motif distance between the important motifs in the promoter sequences of citrate synthase of different mammals. The authors have used a new distance measure to compare the promoter sequences. Results reveal that there exists more similarity between organisms in the same chromosome.