A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

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We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and ... continued below

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Price, Morgan N.; Huang, Katherine H.; Alm, Eric J. & Arkin, Adam P. December 1, 2004.

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We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.

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  • Journal Name: Nucleic Acids Research; Journal Volume: 33; Journal Issue: 3; Related Information: Journal Publication Date: 02/08/2005

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  • Report No.: LBNL--56902
  • Report No.: NAR-02000-S-2004.R2
  • Grant Number: DE-AC02-05CH11231
  • Office of Scientific & Technical Information Report Number: 859714
  • Archival Resource Key: ark:/67531/metadc779299

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • December 1, 2004

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  • Dec. 3, 2015, 9:30 a.m.

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  • April 1, 2016, 8:08 p.m.

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Price, Morgan N.; Huang, Katherine H.; Alm, Eric J. & Arkin, Adam P. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes, article, December 1, 2004; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc779299/: accessed December 18, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.