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Nucleic Acids Research, 2001, Vol. 29, No. 5 1216-1221
© 2001 Oxford University Press

Prediction of operons in microbial genomes

Maria D. Ermolaeva*, Owen White and Steven L. Salzberg

The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

Operon structure is an important organization feature of bacterial genomes. Many sets of genes occur in the same order on multiple genomes; these conserved gene groupings represent candidate operons. This study describes a computational method to estimate the likelihood that such conserved gene sets form operons. The method was used to analyze 34 bacterial and archaeal genomes, and yielded more than 7600 pairs of genes that are highly likely (P >= 0.98) to belong to the same operon. The sensitivity of our method is 30–50% for the Escherichia coli genome. The predicted gene pairs are available from our World Wide Web site http://www.tigr.org/tigr-scripts/operons/operons.cgi.

* To whom correspondence should be addressed. Tel: +1 301 610 5942; Fax: +1 301 838 0208; Email: mariae{at}tigr.org


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