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MBE Advance Access published online on July 21, 2007
Molecular Biology and Evolution, doi:10.1093/molbev/msm145
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© 2007 The Authors
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.

Research Article

A Unified Model Explaining the Offsets of Overlapping and Near-overlapping Prokaryotic Genes

Carl Kingsford{dagger},*, Arthur Delcher{dagger} and Steven L. Salzberg{dagger}

{dagger} Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD. adelcher{at}umiacs.umd.edu, salzberg{at}umiacs.umd.edu

* Corresponding author. Phone: (301) 405-7395; Fax: (301) 314-1341; Postal: Center for Bioinformatics and Computational Biology, Biomolecular Sciences Bldg. #296, University of Maryland, College Park, MD 20742, carlk{at}umiacs.umd.edu

Received for publication April 12, 2007. Revision received June 28, 2007. Accepted for publication July 3, 2007.

Overlapping genes are a common phenomenon. Among sequenced prokaryotes, more than 29% of all annotated genes overlap at least one of their two flanking genes. We present a unified model for the creation and repair of overlaps among adjacent genes where the 3' ends either overlap or nearly overlap. Our model, derived from a comprehensive analysis of complete prokaryotic genomes in GenBank, explains the non-uniform distribution of the lengths of such overlap regions far more simply that previously proposed models. Specifically, we explain the distribution of overlap lengths based on random extensions of genes to the next-occurring downstream stop codon. Our model also provides an explanation for a newly observed (here) pattern in the distribution of the separation distances of closely spaced, non-overlapping genes. We provide evidence that the newly described biased distribution of separation distances is driven by the same phenomenon that creates the uneven distribution of overlap lengths. This suggests a dynamic picture of continual overlap creation and elimination.

Key Words: Genome Analysis • Gene Finding • Overlapping Genes • Prokaryotes


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