Question1: The online programs,PlantCARE (http://bioinformatics.

psb.ugent.be/webtools/plantcare/html/) (Lescot

et al. 2002), NSITE-PL and ScanWM-P (Softberry, http://

linux1.softberry.com/berry.phtml), may be helpful. 

Question2: It replies on the cases of the promoter. I think the figure you presented just a schematic diagram for the promoters.

Question3: I think the it is a combination figure.

I hope my answers could be helpful. Good luck!

@Huiquan Zheng I need the same  size of promoter e.g. at least 1800 bp before start codon, but here in my case i find such promoters whose length is smaller than 800 bp, what should I do in this case? 

Hi,

My bias is that regulatory element bioinformatics predictions need to be experimentally confirmed by something like ChIP-seq or ChiP-PCR. The size of a promoter can vary from gene to gene but genome wide for a mammal it is usually considered to extend -2kb to +0.5kb.

@Ross L Tellam  Except ChIP-seq or ChiP-PCR is there is another way to confirm? What should I do now to equalize every gene promoter start? other wise it will be confusing in making above diagram. Thanks

Hi,

re confirmation: One could also perform mobility shift assays and even pull downs for specific TFs.

Re: diagram. The comparisons should be centered by reference to the TSS not the ATG start codon as the two can be very different. The size of the promoter can be variable if their are practical limits regarding analysis of specific genes. The key feature of the predictions is the FDR value as some TF binding sites have low complexity and therefore a high false discovery rate.

I agree with Ross L Tellam. The promoter region should be calculated started from TSS (Transcription start site), not the ATG. The region between TSS and ATG is the 5'UTR, and this region also varies among genes. 

In additon, there has no any definiation of the exact end of the promoter. Sometimes, a short promoter region (e.g. 800bp) is enough to fulfill its function. 

xie xie ni Huiquan Zheng & Ross L Tellam thanks alot for your explaination.