A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

Journal Article · Wed Dec 01 04:00:00 EST 2004 · Nucleic Acids Research

OSTI ID:859714

Price, Morgan N; Huang, Katherine H; Alm, Eric J; Arkin, Adam P

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.

• Research Organization: Ernest Orlando Lawrence Berkeley NationalLaboratory, Berkeley, CA (US)
• Sponsoring Organization: USDOE Director. Office of Science. Office of Biological andEnvironmental Research, Genomes to Life Program
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 859714
• Report Number(s): LBNL--56902; NAR-02000-S-2004.R2; BnR: KP1102010
• Journal Information: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 3 Vol. 33; ISSN 0305-1048; ISSN NARHAD
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ACCURACY
BACILLUS
BACILLUS SUBTILIS
ESCHERICHIA COLI
GENES
Operons Comparative Genomics