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Asymmetric directional mutation pressures in bacteria

Jean R Lobry* and Noboru Sueoka

Genome Biology 2002, 3:research0058-research0058.14 doi:10.1186/gb-2002-3-10-research0058

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BioMed Central: 9 citations

Research article   Open Access

Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index

Kazuharu Arakawa, Haruo Suzuki, Masaru Tomita BMC Genomics 2009, 10:640 (30 December 2009)

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Research article   Open Access

A comparative approach to elucidate chloroplast genome replication

Neeraja M Krishnan, Basuthkar J Rao BMC Genomics 2009, 10:237 (20 May 2009)

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Research article   Open Access

Comparison of methods for estimating the nucleotide substitution matrix

Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A Huttley, Manuel E Lladser, Rob Knight BMC Bioinformatics 2008, 9:511 (1 December 2008)

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Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes

Richard A Morton, Brian R Morton BMC Genomics 2007, 8:369 (12 October 2007)

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Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

Feng-Biao Guo, Xiu-Juan Yu BMC Genomics 2007, 8:366 (10 October 2007)

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Research article   Open Access

Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes

Chi Chen, Carton W Chen BMC Genomics 2007, 8:286 (21 August 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | Editor’s summary

Diverse patterns of GC/AT skew in bacterial chromosomes reveal the mutation and selection pressures associated with replication and transcription, which may reflect differences in the chromosome replication machinery of different species.

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Using the nucleotide substitution rate matrix to detect horizontal gene transfer

Micah Hamady, M D Betterton, Rob Knight BMC Bioinformatics 2006, 7:476 (26 October 2006)

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Errors in detecting horizontal gene transfer are substantially lower when traditional nucleotide composition methods are combined with a novel approach based on changes in nucleotide substitution rates.

Research article   Open Access

Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics

Alex Mira, Ravindra Pushker, Boris A Legault, David Moreira, Francisco Rodríguez-Valera BMC Evolutionary Biology 2004, 4:50 (26 November 2004)

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Fusobacteria are related to Firmicutes, but over a third of the genes may have been transferred from bacteria within the dental plaque, with many of the genes for cell wall components apparently deriving from proteobacteria.

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Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

Xiu-Feng Wan, Dong Xu, Andris Kleinhofs, Jizhong Zhou BMC Evolutionary Biology 2004, 4:19 (28 June 2004)

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