title: Scoring schemes of palindrome clusters for more sensitive prediction of replication origins in herpesviruses.
abstract: Many empirical studies show that there are unusual clusters of palindromes, closely spaced direct and inverted repeats around the replication origins of herpesviruses. In this paper, we introduce two new scoring schemes to quantify the spatial abundance of palindromes in a genomic sequence. Based on these scoring schemes, a computational method to predict the locations of replication origins is developed. When our predictions are compared with 39 known or annotated replication origins in 19 herpesviruses, close to 80% of the replication origins are located within 2% of the genome length. A list of predicted locations of replication origins in all the known herpesviruses with complete genome sequences is reported.
authors.affiliation: Department of Mathematics, National University of Singapore Singapore. matchewd@nus.edu.sg
authors.forename: David S H
authors.initials: DS
authors.lastname: Chew
authors.forename: Kwok Pui
authors.initials: KP
authors.lastname: Choi
authors.forename: Ming-Ying
authors.initials: MY
authors.lastname: Leung
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004279:DNA, Viral / Q000737:chemistry; D003627:Data Interpretation, Statistical; D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D006564:Herpesviridae / Q000235:genetics*; D018741:Replication Origin; D015203:Reproducibility of Results
chemical_list: D004279:DNA, Viral