Entering edit mode
9.4 years ago
anp375
▴
190
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.
What is it that you want to get? The sequences of the CCDS transcripts, or something else?