title: Nucleotide correlation based measure for identifying origin of replication in genomic sequences.
abstract: Computational prediction of the origin of replication is a challenging problem and of immense interest to biologists. Several methods have been proposed for identifying the replicon site for various classes of organisms. However, these methods have limited applicability since the replication mechanism is different in different organisms. We propose a correlation measure and show that it is correctly able to predict the origin of replication in most of the bacterial genomes. When applied to Methanocaldococcus jannaschii, Plasmodium falciparum apicoplast and Nicotiana tabacum plastid, this correlation based method is able to correctly predict the origin of replication whereas the generally used GC skew measure fails. Thus, this correlation based measure is a novel and promising tool for predicting the origin of replication in a wide class of organisms. This could have important implications in not only gaining a deeper understanding of the replication machinery in higher organisms, but also for drug discovery.
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India. kkshah@mail.jnu.ac.in
authors.forename: Kushal
authors.initials: K
authors.lastname: Shah
authors.forename: Annangarachari
authors.initials: A
authors.lastname: Krishnamachari
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004261:DNA Replication; D004269:DNA, Bacterial / Q000235:genetics; D018744:DNA, Plant / Q000235:genetics; D016054:DNA, Protozoan / Q000235:genetics; D016680:Genome, Bacterial; D018745:Genome, Plant; D018503:Genome, Protozoan; D017015:Methanococcales / Q000235:genetics; D008957:Models, Genetic; D010963:Plasmodium falciparum / Q000235:genetics; D018087:Plastids / Q000235:genetics; D018741:Replication Origin; D014026:Nicotiana / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D018744:DNA, Plant; D016054:DNA, Protozoan