Segmental Duplications for dog

[Arumilli, Meharji]

Dear all,

Could you help us to find the Segmental Duplications table to download
for canFam3.1 assembly? I would like to access the regions defined in
the link
(https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=genomicSuperDups)
for dog genome.

Br
Mehar

[Matthew Speir]

Hello Mehar,


Thank you for your question about a "Segmental Duplications" track for the dog/canFam3 assembly.

We do not have a "Segmental Duplications" track for the canFam3 assembly. The data for these tracks is provided by the Eichler lab at the University of Washington, http://eichlerlab.gs.washington.edu/. Based on the information on their "databases" page, http://eichlerlab.gs.washington.edu/database.html, it looks like most dog assembly with segmental duplication data is the July 2004 assembly, which corresponds to canFam1 in the UCSC Genome Browser, http://genome.ucsc.edu/cgi-bin/hgGateway?db=canFam1.

You will need to contact the Eichler lab about plans for producing this data for the Sep. 2011/canFam3 assembly. You can find contact info for the lab here: http://eichlerlab.gs.washington.edu/curmem.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group