I would like to compare protein domains from transposable elements in human and primates (for example I would like to compare gag and pol from all LTR retrotransposons in human). So far I was thinking about 2 ways:
1, hard way - find ORFs and then do something like conserved domain search
2, run LTRfinder, LTRdigest (I am having problems adding HMM functionality) or some software like this, which might be less sensitive (especially LTR finder was not able to satisfactorily identify protein domains)
3, download annotated elements (is there something like this?)
To sum it up, I would be happy to have sequences of all gag/pol genes from human (and primates).
Thank you very much for your help.