In Silico Prediction of the Origin of Replication among Bacteria: A Case Study of Bacteroides thetaiotaomicron

Albert Pallejà Caro, Eduard Guzman, Santiago Garcia-Vallvé, Antoni Romeu

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

The initiation of chromosomal replication occurs only once during the prokaryote cell cycle. Some origins of replication have been experimentally determined and have led to the development of in silico approaches to find the origin of replication among other prokaryotes. DNA base composition asymmetry is the basis of numerous in silico methods used to detect the origin and terminus of replication in prokaryotes. However, the composition asymmetry does not allow us to locate precisely the positions of the origin and terminus. Since DNA replication is a key step in the cell cycle it is important to determine properly the origin and terminus regions. Therefore, we have reviewed here the methods, tools, and databases for predicting the origins and terminuses of replication, and we have proposed some complementary analyses to reinforce these predictions. These analyses include finding the dnaA gene and its binding sites; making BLAST analyses of the intergenic sequences compared to related species; studying the gene order around the origin sequence; and studying the distribution of the genes encoded in the leading versus the lagging strand.
Original languageEnglish
JournalO M I C S: A Journal of Integrative Biology
Volume12
Issue number3
Pages (from-to)201-210
ISSN1557-8100
DOIs
Publication statusPublished - 2008
Externally publishedYes

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