[Bioperl-l] Fwd: [Bioperl-guts-l] How to obtain all x-linked genes from human genome?

[Sean Davis]

On 10/4/05 3:52 PM, "Heikki Lehvaslaiho" <heikki.lehvaslaiho at gmail.com>
wrote:

> 
> 
> ----------  Forwarded Message  ----------
> 
> Subject: [Bioperl-guts-l] How to obtain all x-linked genes from human genome?
> Date: Tuesday 04 October 2005 18:34
> From: Sally Li <sallyli97 at yahoo.com>
> To: Hilmar Lapp <hlapp at gnf.org>
> Cc: bioperl-guts-l at bioperl.org
> 
> Hi,
> 
> Could some one know how to obtain all gi numbers (gene
> ID in GenBank) of x-linked genes from human genome?

The file gene2refseq.gz located here:

ftp://ftp.ncbi.nih.gov/gene/DATA/gene2refseq.gz

contains information regarding Refseqs (and the associated Gis).  The data
structure is described here:

ftp://ftp.ncbi.nih.gov/gene/DATA/README

Human tax_id is 9606.  GI numbers are there for the refseq sequences.  If
you need more sequences, you could get the genbank accessions from UCSC
using the table browser and limiting to the x-chromosome, but I'm not sure
if/where they store the GI numbers.

Sean