Hi, I'm working on a perl module that can handle a CCDS file: http://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi

I'm mostly done but what's pretty ironic is that I don't really know how a CCDS file is used, since recieved the names and descriptions of required methods from my professor. This is my understanding:

The way I see it, a user and use an entrez gene id or hgnc gene name to get a list of CCDS ids. Then, the corresponding accession numbers of those ids can be used to download the chromosome (versions? I think NC_000001.8, NC_000001.11, and NC_000001.9 all download chromosome 1 though the length differs sometimes.) from Genbank.

Then the gene coordinates and exons are then used to extract the actual sequences.

Is this right?

Thank you.