Computational approach towards promoter sequence comparison via TF mapping using a new distance measure

Abstract

We propose a method for identifying transcription factor binding sites (TFBS) in the given promoter sequence and mapping the transcription factors (TFs). The proposed algorithm searches the +1 transcription start site (TSS) for eukaryotic and prokaryotic sequences individually. The algorithm was tested with sequences from both eukaryotes and prokaryotes for at least 9 experimentally verified and validated functional TFs in promoter sequences. The order and type of TF binding to the promoter of genes encoding central metabolic pathway (CMP) enzyme was tabulated. A new similarity measure was devised for scoring the similarity between a pair of promoter sequences based on the number and order of motifs. Further, these were grouped in clusters considering the scores between them. The distance between each of the clusters in individual pathway was calculated and a phylogenetic tree was developed. This method is further applied to other pathways such as lipid and amino acid biosynthesis to retrieve and compare experimentally verified and conserved TFBS.

Comparison of Promoter Sequences Based on Inter Motif Distance

“…The analysis of promoters for organizational features provides a link between the genomic nucleotide sequence and important aspects of gene regulation and expression. In this work we have attempted to find the positional constraint of some motifs and also inter-motif distance constraint between few motifs of citrate synthase which is present in the citric acid cycle (Krebs cycle) of Central metabolic pathway since this pathway is present in almost all organisms of prokaryotes and eukaryotes Also, we have proposed to find the distance between promoter sequences of different mammals based on cis regulatory module using a distance measure (Meera, Rangarajan, & Bhat, 2009).…”

“…Xie et al (2005) have reported such a large number of motifs in the human genome based on multiple genome comparison . In this work, we have proposed to investigate the inter motif distance between the important motifs in the promoter sequences of citrate synthase of different mammals using a distance measure proposed by Meera, Rangarajan, and Bhat (2009).…”