I'm using mouse mm10. The RepeatMasker track on the UCSC Genome Browser categorizes each repeat with a name, class, and family (there are ~1500 different repeat names, 10 classes and ~50 families). RepBase uses an ID and one or more keywords. I know there's not a one to one relationship between the two databases (http://www.repeatmasker.org/faq.html#faq4) but I'm wondering if it's possible to at least assign a RepeatMasker class and family to each Repbase entry. Is there a tool or database already available that can do this?
Trying some myself, sometimes it's easy like when there's a perfect match between a RepeatMasker name and a RepBase ID. Sometimes the keywords for a RepBase record match one or more RepeatMasker classes or families so it's ambiguous. Sometimes the keywords are similar but not identical to a RepeatMasker class or family so while I could probably determine a pairing by manually looking it, automating it (with a script) is difficult.
