[Genome] [no subject]

[Ann Zweig]

Hello Rachel,

	First let's make sure we are looking at the same position.  The human 
alpha-globin gene cluster is located on chromosome 16 at about: 
chr16:155,973-167,530.  Is this the area you are interested in?  Now, I 
will address your questions one-by-one.


First.
I see a short span in the Conservation track where the mouse line is 
blank, but I do not see such a span in the rat.  The blank area in the 
mouse is at approximately chr16:159,527-160,355.  In this case, there 
just isn't any sequence in the mouse that aligns to the human sequence 
in that location.


Second.
Use the Table Browser to download the aligning sequence (press Tables in 
the blue navigation bar).  Configure it like so:

genome: Human
assembly: Mar 2006
group: Comparative Genomics
track: Conservation
table: multiz17way
region: (choose the region in which you are interested)
output format: MAF

To read more about the MAF file format see this FAQ: 
http://genome.ucsc.edu/FAQ/FAQformat#format5


Third.
No.  However, we do have a TFBS track.  Turn on the track named: TFBS 
Conserved.  This track contains the location and score of transcription 
factor binding sites conserved in the human/mouse/rat alignment.


	I hope this is helpful to you.


Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

We invite you to give us your feedback on the UCSC Genome Browser 
through May 31, 2007: http://www.surveymonkey.com/s.asp?U=881163743177




> Subject:
> From:
> Rachel.J.West at Dartmouth.EDU (Rachel J. West)
> Date:
> 02 May 2007 15:04:01 -0400
> To:
> genome at soe.ucsc.edu
> 
> 
> Hi there-
> 
> I have just begun using your Genome Browser, and although I have found 
> it helpful, I have some questions.
> 
> First- I am examining a noncoding region around the alpha-globin 
> cluster, looking for regions of conservation between humans and other 
> vertebrates. In the alignment display, there are dots, dashes, and 
> double-dashes- all of which I understand. But what does a 'blank' mean? 
> For instance, mouse and rat are both blank this region, though I believe 
> their genomes are fully sequences; is the area siimply too divergent?
> 
> Second-I would like to download the sequence in this region for each of 
> the organisms for which there is some similarity; how do I do that?
> 
> Third- is there a search engine embedded in your program that will 
> search for potential transcription-factor-binding sites, and tell me 
> what they are?
> 
> Thank you! I'll look forward to your response.
> 
> R