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Briefings in Bioinformatics Advance Access published online on April 17, 2008
Briefings in Bioinformatics, doi:10.1093/bib/bbn019
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

The relative value of operon predictions

Rutger W. W. Brouwer, Oscar P. Kuipers and Sacha A. F. T. van Hijum

Corresponding authors. Oscar P. Kuipers and Sacha A. F. T. van Hijum, Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, Kerklaan 30, 9751 NN Haren, University of Groningen. E-mail: o.p.kuipers{at}rug.nl or s.a.f.t.van.hijum{at}rug.nl

For most organisms, computational operon predictions are the only source of genome-wide operon information. Operon prediction methods described in literature are based on (a combination of) the following five criteria: (i) intergenic distance, (ii) conserved gene clusters, (iii) functional relation, (iv) sequence elements and (v) experimental evidence. The performance estimates of operon predictions reported in literature cannot directly be compared due to differences in methods and data used in these studies. Here, we survey the current status of operon prediction methods. Based on a comparison of the performance of operon predictions on Escherichia coli and Bacillus subtilis we conclude that there is still room for improvement. We expect that existing and newly generated genomics and transcriptomics data will further improve accuracy of operon prediction methods.

Keywords: operon, computational prediction, bioinformatics

Submitted: January 11, 2008. Received (in revised form): March 21, 2008.


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