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how to find promoter - (Nov/02/2008 )

hi, guys!
if I get the whole sequence of a gene and its CDS sequence, how to know the exact location and range of its promoter?


The promoter is not included in the CDS (Coding Domain Sequence). You'll have to get some sequence upstream of the start codon, unless the gene is part of an operon, then you'll have to find the first gene of the operon, and look upstream of it.


There are many free softwares just blast your sequence ...


In arabidopsis, I often take the 1.5kb upstream of the start coden of the gene. I think it will contain the promoter except some cases that the promoter is somewhere else far away from the CDS.