how to find a binding site in genes - help, please (May/23/2006 )

Hi, I want to ask if some one know how to perform and simple search of binding sites of certain transcription factor in some genes, I want just to look quickly, if the genes that codify some voltage dependent channels (calcium channel in specific...) have in their sequence a binding site for a transcription factor, I am thinking that may be some kind of program can help me, but I am not so sure.

Somebody knows how to check this in a simple way....

i am studing in specific the calcium voltage channels, so i need to work in the gene.

Google has lots of Transcription Factor binding site sites (pardon the unfortunate repetition). However most of them use algorithms which don't always provide the most intelligible results.

Your best best would be to use Pubmed and search for occurrences of your TF of interest and your gene promoter. Then again Google might know the answer to that as well. Jeeves wouldn't!

There are lots of web-based algorithms available to give you the information you'll need. Many of them can be found at this BU website:

http://zlab.bu.edu/zlab/gene.shtml

Also you can get a trial to the Genomatix suite of programs and use their promoter prediction tool, which I've always liked.

THANK YOU SO MUCH FOR THE INFORMATION, I AM GOING TO STAR SEARCHING....