Predicting promoter regions for ncRNA in bacteria. I am looking for a promoter of a certain RNA I know the sequence and locus of.
Thanks, I actually gave BPROM (link below) a shot and seems to confirm the start site I had in mind. Too bad the tool appears to be closed source.
I also whish I could cite the article that is listed as reference, but I cannot find the original.
http://linux1.softberry.com/berry.phtml?topic=bprom&group=programs&subgroup=gfindb
We can scan your regulatory region by PlatProm (Shavkunov et al. NAR 2009, 37, 4919). Soon, the software will be available on line, but until then you can contact me personally ([email protected]).
BPROM should be fine. There is nothing special in the promoter of non-coding RNAs. If you are trying to determine whether an intergenic region contains a non-coding RNAs, looking for the classical stem-loop structure of a Rho-independent terminator might be easier.
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