I am trying to predict the promoter and terminator of Fum 9 and Fum10 (Fusarium verticillioides) with a software. I include 500bp upstream of ORF. Different promoter prediction softwares were tried but none of them worked. I am wondering how people normally predict the promoter sequence? Thank you very much.
I think that usally people take the region upstream their gene of interest and define an arbitrary length of the promoter... Usually 1500 to 2000 bp
Hi, I agree with David. Usually I define the initial transcription start point and afterwards I take around 1000bp and look for promoter elements (PLACE is a good program).
Hi Nanxi,
I just come across a new review about in-silico promoter identification that you might find useful for your analysis:
In silico Identification of Eukaryotic Promoters
VR Yella, M Bansal - Systems and Synthetic Biology, 2015
Anyway, promoter prediction is a tricky business, good luck with your work!
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