In silico Detection of Origins of Replication in Bacteria and Archaea

Abstract

In this paper we have studied the replication machinery in three domains of life namely, Bacteria, Archaea and Eukaryotes. We have
discussed the in silico methods which are being used for locating Ori (origin of replication) sites in Bacteria and Archaea. We have also shown that some nucleotide skew method namely GC skew is good enough to locate the Ori site in bacteria but it fails in Archaea because the Archaea do not have pronounced nucleotide skew. It has been observed that combined strategy of cumulative GC skew and DnaA boxes location can improve results for bacterial genomes. Data show that bacterial replication proteins tend to lie in cluster adjacent to each other. The use of Z curve, location of cdc6 gene, upstream AT rich region and consensus ORB sequences can help us to increase the confidence level in detecting the Ori sites in Archaea. We have also found that copy number and position of cdc6 gene correlated directly with the Ori site in Archaea.