Publication: Operons Across Prokaryotes: Genomic Analyses and Predictions 300+ Genomes Later

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Title Operons Across Prokaryotes: Genomic Analyses and Predictions 300+ Genomes Later
Authors/Editors* G Moreno-Hagelsieb
Where published* Current Genomics
How published* Journal
Year* 2006
Volume 7
Number 3
Pages 163-170
Publisher Bentham Science Publishers Ltd
Keywords Operon predictions, inter-genic distance, conservation of gene order, phylogenetic profiles
With operon predictions based on conservation of gene order and 330 Prokaryotic genomes available, I am able to show that in most of the genomes analyzed about 70% of the genes in operons are separated by distances of -20 to 30 base pairs. Most of the differences in this tendency might be related to the appearance of signals inside the operons. How- ever, a closer look at the extreme exceptions confirms that annotation problems are partly responsible for inter-genic dis- tance distributions that deviate from that of operons in Escherichia coli K12. I also argue that the inter-genic distances of adjacent genes in different transcription units (transcription unit boundaries or TUBs) should be expected to be more vari- able than those for genes in the same operon. Using phylogenetic profiles I show that predictions adjusted on a per ge- nome basis might help increase the accuracy of operon predictions. Improvements in automated annotation might be nec- essary to fully evaluate the overall tendencies of genes in operons towards short inter-genic distances, and to better under- stand differences in regulatory complexity across Prokaryotes.
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