[Genome] Conserverd Regions

[Brooke Rhead]

Hello Mayra,

You can get conserved sequence for your region of interest via the Table 
Browser.  Hit the "Tables" link at the top of the page and make the 
following selections:

clade: vertebrate
genome: human
assembly: Mar. 2006 (or whichever assembly you wish to use)
group: comparative genomics
track: conservation
region: choose "position" and enter chrX:65151000-65152122 in the box
output format: MAF - multiple alignment format

Also enter a filename in the "output file" box if you want to download 
the data to your computer.

Hit "get output".  You should see the aligning sequence in MAF format 
(MAF is described here: http://genome.ucsc.edu/FAQ/FAQformat#format5). 
Note that, like nearly all of the formats available in our databases, 
the start coordinates in MAF are 0-based, not 1-based.  An explanation 
is here: http://genome.ucsc.edu/FAQ/FAQtracks#tracks1.

I hope this information helps.  If you have further questions, pleas do 
not hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Mayra Eduardoff wrote:
> Hi,
> Is there any  "easy" way I can download the sequences of conserved regions
> between species for a specific ie. human DNA region ? Ie. I am looking to
> download all DNA sequences aligned to the human genome region of chromosome
> X between bp  65151000 and 65152122.
> many thanks in advance
> 
> Mayra  Eduardoff
> (Tyrolean Cancer Research Institute)
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome