I am interested in analyzing the promoter sequences of plant genes for regulatory elements, especially during the seed development. I am working with several plants, mostly dicots.
Hi Hirotada, I use SoftBerry.
Here is the link: http://linux1.softberry.com/berry.phtml?topic=tssp&group=programs&subgroup=promoter
It will give you putative positions of promoters, enhancers and transcription factor binding sites. All well explained in the Help and Example file. All best.
Nada. Thank you. Somehow, I did not get any email about your answer so I did not know it until today. TSSP finds a lot of TF binding sites, but the results did not offer links to explain what they were. I tried NSITE-PL also, but it showed the results with animal transcription regulatory elements instead of plant TREs somehow. Any way, thanks.
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