[Genome] finding breaks in human-other synteny

[Ann Zweig]

Hello aDNAn,

	We have a couple of tracks on most of our browsers that will give you the 
information you need.  If you were interested in getting a list of positional 
information instead of simply visualizing the information in the browser, let me 
know and I will give you instructions for that as well.

	To visualize the syntenic breakpoints in the browser, follow these steps.  I 
will explain how to do this for the latest human assembly (hg18) and the latest 
cow assembly (bosTau2), but you can of course use any pair of organisms.

1. Open the hg18 browser.

2. Hide all of the tracks except the Conservation track (set visibility to 
full), the Cow Chain (set visibility to dense), and the Cow Net (set visibility 
to full).

3. From the configuration page for the Conservation track (press the 
'conservation' link from the track controls), un-check all organisms except the cow.

	The Net track will give you the information you want.  This track shows the 
best cow/human chain for every part of the human genome. It is useful for 
finding orthologous regions and for studying genome rearrangement.  You can read 
more about how to interpret the Net track on the details page (click on the "Cow 
Net" link from the track controls).

	The best chains are displayed on "Level 1" in the Net track.  The gaps from 
Level 1 are filled in with other chains that are displayed on "Level 2" (and so 
on).  If the chain on a lower level is on the same chromosome as the chain on 
the level above it, it is syntenic.  Other possibilities are inversions, or 
non-syntenic chains.

	A particularly good example is the following region in human: 
chrX:152,048,252-152,052,811.  If you view the Cow Net track for this region, 
you can see that there are three distinct orthologous regions in the bosTau2 genome:

scaffold9234
scaffold14102
scaffold10843

	This should get you started.  As I said, if you would like to generate a list 
of syntenic regions using the Table Browser, feel free to write back to this list.


Regards,

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




Adnan Derti wrote:
> Hello.
> 
> I'd like to infer breakpoints in synteny between two genomes. Could you 
> recommend a simple method or a set of rules of thumb based on your 
> alignments of orthologous regions? The results don't need to be precise.
> 
> As always, thank you for the data and answers you provide.
> 
> aDNAn Derti
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome