[Genome] mouse genome

[Hiram Clawson]

Good Morning Greg:

I'm not sure what kind of sequence you need for your research, but
there are a number of methods to fetch sequence.

You can fetch the chromosome fasta files directly from the
downloads server:
	ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/

If you want to fetch particular locations of sequence, you
can define the chrom,start,end locations in a bed file:
	http://genome.ucsc.edu/FAQ/FAQformat#format1
and load that bed file into the genome browser as a custom
track, then have the table browser return that track to
you as fasta sequence.

If your searching for sequence is going to be extensive,
you could use the kent source tree tools to pick apart
fasta files or the mm9.2bit file:
http://genome.ucsc.edu/admin/cvs.html
http://genome.ucsc.edu/admin/jk-install.html
ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit

The sequence is not available via the public MySQL server since
we do not keep the sequence in MySQL tables.

--Hiram

gbr0wn at comcast.net wrote:
> I would like to download the mouse chr7 sequence to search for restriction sites.  The only available table ("gold") had sequence data but only in blocks of ~150,000 bp separated by descriptive text, such as:
>  >mm9_gold_CAAA01093116.1 range=chr7:3467421-3470303 5'pad=0 3'pad=0 revComp=TRUE strand=- repeatMasking=none
> 
> which seems to be messing up the bioperl routine I'm using to find restriction sites.  Is there a way to download the sequence without the interfering text?
> 
> Thanks, Greg Brown