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MBE Advance Access originally published online on July 21, 2007
Molecular Biology and Evolution 2007 24(9):2091-2098; 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 Articles

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

Carl Kingsford, Arthur L. Delcher and Steven L. Salzberg

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland

E-mail: carlk{at}umiacs.umd.edu.

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 1 of their 2 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 nonuniform distribution of the lengths of such overlap regions far more simply than 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 nonoverlapping 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

Jennifer Wernegreen, Associate Editor


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