Which is the best tool for operon prediction in bacteria?

27 September 2013 1 3K Report

I am analyzing a bacterial genome recently sequenced in our group. After gene finding and annotation I would have a rough overview of its operon structure using a bioinformatic software. Can anyone suggest a tool to perform this analysis?

Jonathan David Moore

I came across this paper a while ago relating to Streptomyces coelicolor: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2175336

My understanding is that predicted TFBS, size of gap between coding regions, and expression data across multiple conditions should give a good prediction. I'm not sure what organism you are working on, but my understanding is that things are quite different in S.coelicolor from what might be expected using E.coli as a model, and far fewer strict operons are observed. Sorry I can't offer a reference for that.

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