Mouse strain assembly hub - May 3, 2017

This assembly hub contains 16 different strains of mice as the primary sequence, along with strain-specific gene annotations. Viewing this assembly hub on mm10, there will be a multiple alignment between the reference and 16 different strains of mice plus rat. The creation of this hub was made possible thanks to the Mouse Genomes Project.

How to view the hub

You can easily load this hub from our Public Hubs page or by clicking these links to any of our official websites:

• genome.ucsc.edu
• genome-euro.ucsc.edu
• genome-asia.ucsc.edu

To manually attach this hub to other genome browsers:

1. From the blue navigation bar, go to My Data -> Track Hubs
2. Then select the My Hubs tab and enter this URL into the textbox:
   http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt
3. Once you have added the URL to the entry form, press the Add Hub button to add the hub.

After adding the hub, you will be redirected to the mm10 gateway page. To view one of the new mice strains as the primary sequence, at the top of the phylogenetic tree diagram on the gateway page, click on mouse strain assemblies (16). This will allow you to choose between the 16 different strains from the drop-down menu.

Data resource links

Note: In the browser, insertions may be missing from visualizations for alignments between these strains due to missing 'i' rows in the MAF files for these mouse strain assemblies.