5.3 years ago by
You can get ancestral repeats from the UCSC table browser. For example, if you want ancestral repeats for human and mouse, referenced to the human hg19 build, you would select genome="human", assembly="Feb 2009 (GRCh37/hg19), group="Repeats", track="RepeatMasker", then click the "Create" button in the intersection area. On the Intersect With RepeatMasker page this takes you to, you would select group="Comparative Genomics", track="Placental Chain/Net", table="Mouse Chain (chainMm10)", select the radio button for "All RepeatMasker records that have at least [XX]% overlap with Placental Chain/Net" and set XX=100 (which implies the whole RepeatMasker element must exist in both species' sequence). Click "submit" at the bottom and, back on the main Table Browser page, put in whatever options you want for your output (send to browser, save as file, etc.) and click "Get Ouput". If you want to do this for only a specific region of the genome, you can define the region in the box provided or upload a set of regions you have saved to a file.