Help!!!!!??? Phylocon

[cmnailecin]

Has anyone here every used PhyloCon ( http://www.ncbi.nlm.nih.gov/pubmed/18428790 ) or anything like it.

I am trying to identify conserved promoter regions across a species and I'm completely stuck and I really need to get through this. I have three species that I am using. Currently the format of the files of multiple promoter regions in each file is just plain text. I guess I am stuck in terms of using PhyloCon because I am not sure how to convert my file format into the format necessary for PhyloCon input. This is the link to the sample sequence file that is posted on the website.

http://stormo.wustl.edu/PhyloCon/LEU3.pcons

Any help would be greatly appreciated. Thank you in advanced!