How to detect genes of transposable elements

Question

[shelkmike]

I assembled a genome, masked it with RepeatModeler and RepeatMasker, and then annotated it. However, the repeat masking is not perfect, hence some genes of transposable elements appeared in the annotation.

The problem is that I want to compare protein-coding gene content between this species and a closely related species that has a 3 times smaller genome, and the difference is partially owing to a different number of transposable elements.

So, I want to remove genes of transposable elements from annotations of both genomes. What is a good method to classify protein-coding genes into those that belong to transposable elements and those that do not?