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Briefings in Bioinformatics Advance Access originally published online on July 26, 2008
Briefings in Bioinformatics 2008 9(5):376-391; doi:10.1093/bib/bbn031
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Identification of replication origins in prokaryotic genomes

Natalia V. Sernova and Mikhail S. Gelfand

Corresponding author. M.S. Gelfand, Institute for Information Transmission Problems (the Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetny pereulok, 19, Moscow, 127994, Russia. Tel: +7-495-650-4225; Fax: +7-495-650-0579; E-mail: gelfand{at}iitp.ru

The availability of hundreds of complete bacterial genomes has created new challenges and simultaneously opportunities for bioinformatics. In the area of statistical analysis of genomic sequences, the studies of nucleotide compositional bias and gene bias between strands and replichores paved way to the development of tools for prediction of bacterial replication origins. Only a few (about 20) origin regions for eubacteria and archaea have been proven experimentally. One reason for that may be that this is now considered as an essentially bioinformatics problem, where predictions are sufficiently reliable not to run labor-intensive experiments, unless specifically needed. Here we describe the main existing approaches to the identification of replication origin (oriC) and termination (terC) loci in prokaryotic chromosomes and characterize a number of computational tools based on various skew types and other types of evidence. We also classify the eubacterial and archaeal chromosomes by predictability of their replication origins using skew plots. Finally, we discuss possible combined approaches to the identification of the oriC sites that may be used to improve the prediction tools, in particular, the analysis of DnaA binding sites using the comparative genomic methods.

Keywords: origin of replication, comparative genomics, DnaA-box, genomic composition asymmetry, GC-skew

Submitted: April 8, 2008. Received (in revised form): July 2, 2008.


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