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MBE Advance Access originally published online on August 10, 2005
Molecular Biology and Evolution 2005 22(12):2315-2317; doi:10.1093/molbev/msi231
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org

Letter

How Not to Search for Isochores: A Reply to Cohen et al

Oliver Clay and Giorgio Bernardi

Laboratory of Molecular Evolution, Stazione Zoologica Anton Dohrn, Villa Comunale, Napoli, Italy

E-mail: bernardi{at}szn.it.

In a recent paper in these pages, Cohen et al. search for isochores in the human genome, based on a system of attributes that they assign to isochores. The putative isochores that they find and choose for presentation are almost all below 45% GC and cover only about 41% of the genome. Closer inspection reveals that the authors' methodology systematically loses GC-rich isochores because it does not anticipate the considerable fluctuations and corresponding long-range correlations that characterize mammalian DNA and that are highest in GC-rich DNA. Thus, they over-fragment GC-rich isochores (and also many GC-poor isochores) beyond recognition.

Key Words: base composition • evolution • heterogeneity • long-range correlations


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This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
F. G. Jorgensen, M. H. Schierup, and A. G. Clark
Heterogeneity in Regional GC Content and Differential Usage of Codons and Amino Acids in GC-Poor and GC-Rich Regions of the Genome of Apis mellifera
Mol. Biol. Evol., February 1, 2007; 24(2): 611 - 619.
[Abstract] [Full Text] [PDF]

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 Genome Res.Home page
M. Costantini, O. Clay, F. Auletta, and G. Bernardi
An isochore map of human chromosomes.
Genome Res., April 1, 2006; 16(4): 536 - 541.
[Abstract] [Full Text] [PDF]


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