A novel method for accurate operon predictions in all sequenced prokaryotes.

Abstract:

: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 Helicobacter pylori, 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 six phylogenetically 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 PCC 6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Price MN,Huang KH,Alm EJ,Arkin AP

doi

10.1093/nar/gki232

keywords:

subject

Has Abstract

pub_date

2005-02-08 00:00:00

pages

880-92

issue

3

eissn

0305-1048

issn

1362-4962

pii

33/3/880

journal_volume

33

pub_type

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