Comparison of complete microbial genomes reveals a large number of conserved gene clusters - sets of genes that have the same order in two or more different genomes. Such gene clusters often, but not always represent a co-transcribed unit, or operon. We developed a method to detect and analyze conserved gene pairs - pairs of genes that are located close on the same DNA strand in two or more bacterial genomes. For each conserved gene pair, we calculate an estimate of probability that the genes belong to the same operon. The algorithm takes into account several alternative possibilities. One is that functionally unrelated genes may have the same order due simply because they were adjacent in a common ancestor. Other possibilities are that genes may be adjacent in two genomes by chance alone, or due to horizontal transfer of the gene pair.
The method is modified from the one described in: Maria D. Ermolaeva, Owen White and Steven L. Salzberg. Prediction of Operons in Microbial Genomes. Nucleic Acids Research, 29, 1216-1221, (2001)
Mihaela Pertea, Kunmi Ayanbule, Megan Smedinghoff and Steven L. Salzberg. Prediction of Operons in Microbial Genomes. Nucleic Acids Research, doi:10.1093/nar/gkn784 (2008)
Last update of OperonDB: August 2010.
Click here to see the predicted gene pairs for 1059 bacterial and archaeal genomes.
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