For the study, we have isolated a promoter sequence that has been ligated with Luciferase vector and transfected into the HeLa cells which are being incubated in different experimental conditions. Luciferase assay will be used to predict if the gene had a direct or indirect impact on certain processes on our model organism. For that very purpose, I have been looking for the transcription factors or other motifs that can bind to our promoter sequence, but the search for the software has been in vain. It would be really helpful if anyone could suggest some resources for the prediction.
I found this tool very useful. It gives you a lot of matches, though, so you will have to filter based on what you know is biological meaningful: http://jaspar.genereg.net/
A lit of all available promoter analysis tools is listed here - https://molbiol-tools.ca/Promoters.htm
Personally I used PromoterHunter tool, works fine for me, you could try it out.
Hello,
You can do it using ALGGEN PROMO, it is easy and straight forward just have to put your promoter sequence, indicating the species, factors, and Matrices. It will give you both predicted and validated transcription factors for your sequence.
(http://alggen.lsi.upc.edu/recerca/menu_recerca.html)
Good Luck
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