Is there a tool to look for known or simply conserved promoter regions for non-coding RNA?

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

Olga N Ozoline

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]).

Maulik P Patel

In that case you can use the softberry promoter tools.

Roberto Balbontín

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.

Saravana R K Murthy

Genomatix Software Suite would be an other option.

Manuel Salvador de Lara

I suggest to you prodoric database, where you can find a really long list of bacterial promoters. They are also provided with their respective position weight matrix (PWM). If your bacteria has its genomic sequence available, it could be included in their database and you could also screen along the genome sequence.

http://prodoric.tu-bs.de/

http://prodoric.tu-bs.de/vfp/vfp_regulon.php (for regulon analysis).

http://prodoric.tu-bs.de/vfp/vfp_help.php (tutorial).

I like prodoric because it also provide an extra analysis of the predicted promoters (if the genome sequence is included in its database): "Similar Intergenic Location Analyzer" (SMILE). In SMILE both sequence and positional conservation within an orthologous group of matches can be analyzed. This approach enables the evaluation of putative transcription factor targets and helps to rule out false-positive predictions.

Another interesting webtools are

http://genome2d.molgenrug.nl/index.php/tfbs-search

http://archaea.u-psud.fr/fitbar/

http://regprecise.lbl.gov/RegPrecise/

But their predictions can not be analyzed like the ones provided by prodoric.

Good luck!

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