Nucleic Acids Research Advance Access originally published online on October 25, 2008
Nucleic Acids Research 2008 36(22):e147; doi:10.1093/nar/gkn753
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Nucleic Acids Research, 2008, Vol. 36, No. 22 e147
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes
Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
*To whom correspondence should be addressed. Tel: +1 208 885 4012; Fax: +1 208 885 7905; Email: celesteb{at}uidaho.edu
Received June 26, 2008. Revised September 20, 2008. Accepted October 6, 2008.
Plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. To understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the ‘evolutionary history’ of these plasmids, i.e. the range of hosts in which they have evolved. Since extensive data support the proposal that foreign DNA acquires the host's nucleotide composition during long-term residence, comparison of nucleotide composition of plasmids and chromosomes could shed light on a plasmid's evolutionary history. The average absolute dinucleotide relative abundance difference, termed 
-distance, has been commonly used to measure differences in dinucleotide composition, or ‘genomic signature’, between bacterial chromosomes and plasmids. Here, we introduce the Mahalanobis distance, which takes into account the variance–covariance structure of the chromosome signatures. We demonstrate that the Mahalanobis distance is better than the -distance at measuring genomic signature differences between plasmids and chromosomes of potential hosts. We illustrate the usefulness of this metric for proposing candidate long-term hosts for plasmids, focusing on the virulence plasmids pXO1 from Bacillus anthracis, and pO157 from Escherichia coli O157:H7, as well as the broad host range multi-drug resistance plasmid pB10 from an unknown host.
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