Recently, we assembled a new rodent species and did the genome annotation. We found several gene families are under expansion in the new species. We want to check whether the gene copies in the expanded gene families are pseudogenes or not. I looked at the PseudoPipe (i.e., an automated pseudogene identification pipeline). But it seems I need to provided the functional protein sequences and it will identify pseudogenes in the intergenic regions.
I feel it is not what I want. Firstly, I am not sure whether the annotated genes are really function or not. Secondly, I want to check whether the annotated genes are pseudogenes or not (not looking for pseudogenes in the intergenic regions).
Do anyone have any suggestions on this?