I have to control the expression of a gene ( in vitro ). For designing an optimal promoter assay, I would like to know more about Transcription factor binding region, enhancer and repressor elements on the promoter region.
Can anyone please suggest me good tools or methods to do the same.
Thank you,
There is a well-known motif discovery tool (MEME). In your case, you should provide the sequence of the promoter to know which TF's might bind in there.
Article The MEME suite
http://meme-suite.org/tools/meme
Hi Nikhil,
I recommend using the MatInspector and PromoterInspector tools of the Genomatix software suite. I have used these to analyze TF binding sites and promoter elements, with their location and prediction scores for several mammalian promoters. Hope this helps!
Hi
the UCSC site (http://genome.ucsc.edu) offers you multiple tools in which you'll find a genome browser. with this browser, you'll have the possibility to visualize optional tracks listened in the regulation list (under the browser). this site could also help you in many purposes.
stay safe
fred
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