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Title: A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

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.
Authors:
; ; ;
Publication Date:
OSTI Identifier:
859714
Report Number(s):
LBNL--56902; NAR-02000-S-2004.R2
Journal ID: ISSN 0305-1048; NARHAD; R&D Project: VGTLAA; BnR: KP1102010; TRN: US200524%%25
DOE Contract Number:
DE-AC02-05CH11231
Resource Type:
Journal Article
Resource Relation:
Journal Name: Nucleic Acids Research; Journal Volume: 33; Journal Issue: 3; Related Information: Journal Publication Date: 02/08/2005
Research Org:
Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
Sponsoring Org:
USDOE Director. Office of Science. Office of Biological andEnvironmental Research, Genomes to Life Program
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ACCURACY; BACILLUS; BACILLUS SUBTILIS; ESCHERICHIA COLI; GENES Operons Comparative Genomics