Hierarchy of repeat classes from repeatmasker

Question

[olga.botvinnik]

I'd like to get the hierarchy of mapping classes of repeats to the subgroups in RepeatMasker.

For example, here's the distribution of repeats in Rhesus Macaque: http://www.repeatmasker.org/species/rheMac.html

Here's a screenshot from the website, which shows the hierarchy of repeat classes as "SINE/MIR", indicating that "MIR" is a sublcass of "SINE." Thus, this data exists somewhere on the website, but the trouble is, I can't seem to find this mapping anywhere on repeatmasker.org, but maybe I've just been searching in the wrong places.

Where can the classes of repeats be downloaded from?

Answer 1

[Surya Saha]

You should be able to get the repeat hierarchy from the RepeatMaskerLib.embl file that is distributed as a part of the RepBase library used for this annotation (RepeatMasker Library db20140131).

RepBase libraries are available from GIRI after free registration. http://www.girinst.org/server/RepBase/index.php.

The queryRepeatDatabase.pl script bundled with RepeatMasker may be helpful. Or you could just parse the .EMBL file.