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Nucleic Acids Research 2004 32(18):5392-5397; doi:10.1093/nar/gkh882
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Published online 11 October 2004

Nucleic Acids Research, Vol. 32 No. 18 © Oxford University Press 2004; all rights reserved

Conservation of adjacency as evidence of paralogous operons

Sarath Chandra Janga and Gabriel Moreno-Hagelsieb*

Program of Computational Genomics, CIFN-UNAM, Apdo Postal 565-A, Cuernavaca, Morelos, 62100 Mexico

* To whom correspondence should be addressed at present address: Department of Biology, Wilfrid Laurier University, 75 University Avenue West, Waterloo, ON, Canada N2L 3C5. Tel: +1 519 884 0710 ext. 2364; Fax: +1 519 884 0464; Email: gmoreno{at}wlu.ca

Received June 12, 2004; Revised August 26, 2004; Accepted September 21, 2004

Most of the analyses on the conservation of gene order are limited to orthologous genes. However, the organization of genes into operons might also result in the conservation of gene order of paralogous genes. Thus, we sought computational evidence that conservation of gene order of paralogous genes represents another level of conservation of genes in operons. We found that pairs of genes within experimentally characterized operons of Escherichia coli K12 and Bacillus subtilis tend to have more adjacently conserved paralogs than pairs of genes at transcription unit boundaries. The fraction of same strand gene pairs corresponding to conserved paralogs averages 0.07 with a maximum of 0.22 in Borrelia burgdorferi. The use of evidence from the conservation of adjacency of paralogous genes can improve the prediction of operons in E.coli K12 by ~0.27 over predictions using conservation of adjacency of orthologous genes alone.


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