MicrobesOnline Operon Prediction

Genes which are close together and/or tend to occur in the same vicinity are predicted to be in the same operon. More specifically, we combine predictions from comparative genomics with genome-specific distance models trained on the comparative predictions and their estimated error rates. Our method performs comparably to trained predictions in E.coli and B.subtilis, with accuracy over 80% on candidate operon pairs of genes (adjacent genes on the same strand). Our analysis of microarray data from E.coli, B.subtilis, Helicobacter pylori, Chlamydia trachomatis, Synechocystis sp. PCC 6803, and the archae Halobacterium sp. NRC-1 suggests that our predictions are effective across the prokaryotes. Further information is available here, or contact Eric Alm

MicrobesOnline Operon Viewer

All operon predictions are displayed graphically on the website as part of the locus info page. Experimentally characterized operons are also provided when available.

In the operon viewer, the query gene is shown in navy blue. Nearby genes predicted to be in the same operon are colored in light blue. The next genes upstream and downstream of the operon are are shown in white. The arrowhead indicates the transcription direction. The numbers appear below the genes indicate the intergenic distance between two adjacent genes. Negative numbers indicate overlapping genes. Each gene is labeled by its gene name, synonym or VIMSS locusId, and is hyperlinked to its locus info page.

Updated on March 22, 2005