Promoter Finder - How to find out promoter of known genes (Dec/22/2003 )
From the Genome database or GenBank of NCBI, I can only retrieve the RefSeq for the gene I wanted. I'm wondered how can I get the promoter information of this know gene?
Thanks a lot!
Unfortunately, public genome databases such as NCBI, UCSC and Ensembl have not done promoter annotation to human genome. There are various algorithms for promoter prediction and web servers for you to input a sequence in which you want to find a promoter. I don't know what is your goal to find the promoter sequence. If you want to test if a piece of sequence is characteristic of promoter, you can just use those web servers. If you want to do some gene regulation study such as methyaltion mapping, you better first query Entrez nucleotide sequence database to see if there are experimentally verified promoter sequence for your gene. I must say the query tool is not easy to use and you have to try using different terms such as "promoter", "flanking", etc. in combination of your gene name (again here try exhausting any aliases). You can also search medline to see if someone has cloned and characterized the promoter, if yes, the sequence should have been deposited in GenBank.
For promoter predication, this review may help http://www.cbs.dtu.dk/~gorm/papers/ccrev-pre.pdf
Hope that's useful.
This may help you