finding common tf binding sites for large no. of promoters - is there a program??? (Dec/12/2005 )

I have recently done some large microarray experiments, and am now moving into the scary world of bioinformatics and data mining!!!

I am wanting to look for common transcription factor binding sites in the promoters of genes from my array. I am wondering if anyone knows of a program that I can use that will extract the promoters from a given list of genes and then perform TF binding site searches on all these promoters. As you can imagine I have a very large number of genes I wish to analyse so it is not really practical for my to individually find the promoters of these genes and run individual searches on them.

Any suggestions would be appreciated!
Thanks

I am not sure about this, but you might want to have a look at the programs in the EMBOSS package... there may be something in there that can help you.

just enter EMBOSS into a popular search tool.

www.genomatix.de

some parts of the suite are free, some cost $$$

but, I bet they can do what you want; that suite has everything

thanks heaps!

Hi,

You can try TransFac on TESS: http://www.cbil.upenn.edu/tess/ or Alibaba2: http://www.gene-regulation.com/login

Best,

Megan