A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes

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

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)2091-2098
Number of pages8
JournalMolecular biology and evolution
Issue number9
StatePublished - Sep 2007
Externally publishedYes


  • Gene finding
  • Genome analysis
  • Overlapping genes
  • Prokaryotes

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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