BMC Genomics Research article Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index Kazuharu Arakawa*1, Haruo Suzuki2 and Masaru Tomita1 BioMed Central Open Access Address: 1Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan and 2Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA Email: Kazuharu Arakawa* - gaou@sfc.keio.ac.jp; Haruo Suzuki - hs568@cornell.edu; Masaru Tomita - mt@sfc.keio.ac.jp * Corresponding author Published: 30 December 2009 BMC Genomics 2009, 10:640 doi:10.1186/1471-2164-10-640 This article is available from: http://www.biomedcentral.com/1471-2164/10/640 Received: 19 June 2009 Accepted: 30 December 2009 © 2009 Arakawa et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Due to their bi-directional replication machinery starting from a single finite origin, bacterial genomes show characteristic nucleotide compositional bias between the two replichores, which can be visualised through GC skew or (C-G)/(C+G). Although this polarisation is used for computational prediction of replication origins in many bacterial genomes, the degree of GC skew visibility varies widely among different species, necessitating a quantitative measurement of GC skew strength in order to provide confidence measures for GC skew-based predictions of replication origins. Results: Here we discuss a quantitative index for the measurement of GC skew strength, named the generalised GC skew index (gGCSI), which is applicable to genomes of any length, including bacterial chromosomes and plasmids. We demonstrate that gGCSI is independent of the window size and can thus be used to compare genomes with different sizes, such as bacterial chromosomes and plasmids. It can suggest the existence of different replication mechanisms in archaea and of rolling-circle replication in plasmids. Correlation of gGCSI values between plasmids and their corresponding host chromosomes suggests that within the same strain, these replicons have reproduced using the same replication machinery and thus exhibit similar strengths of replication strand skew. Conclusions: gGCSI can be applied to genomes of any length and thus allows comparative study of replication-related mutation and selection pressures in genomes of different lengths such as bacterial chromosomes and plasmids. Using gGCSI, we showed that replication-related mutation or selection pressure is similar for replicons with similar machinery. Background DNA replication makes up a significant proportion of the bacterial cell cycle, especially in fast-growing bacteria where chromosomes undergo multiple rounds of replica- tion in order to compensate for a short generation time [1]. Therefore, bacterial chromosomes are structured by the requirement to be an efficient medium for replication [2]. Eubacterial species typically have circular chromo- somes that are partitioned into two replichores by one finite set of a symmetrically located replication origin and Page 1 of 10 (page number not for citation purposes)