[Genome] MySQL access to genome browser question

[Hiram Clawson]

Good Afternoon Mike:

No, the genome sequence is not in MySQL.  We keep that in files.
For C. elegans you can pick up the sequence at:
nib files:	ftp://hgdownload.cse.ucsc.edu/gbdb/ce2/nib/
fasta files: ftp://hgdownload.cse.ucsc.edu/goldenPath/ce2/chromosomes/

And then with those files, using the kent source tree
utilities faFrag or nibFrag you can extract any bits of sequence
you want.

This assumes you build the kent source tree:
	http://genome.ucsc.edu/admin/jk-install.html

--Hiram

On 2007 Feb 01, , at 12:22 PM, Michael P. Cary wrote:

> Hi,
>
> Is there a way to retrieve DNA sequences directly from a MySQL query?  
> E.g.,
> is it possible to write a query to retrieve the sequence from C. 
> elegans
> chromosome IV on the positive strand from position 90,232 - 90,554?  I 
> need
> to do this for ~100 or so sequences at a time, so using the manual 
> interface
> is not really an option for me.
>
> Also, is there a FAQ or something that provides more detail on the 
> direct
> MySQL interface?
>
> Thanks,
> Mike