[maker-devel] gene duplicates and track the query protein

[Zhou Qi]

Dear maker users and developers:

I'm new to maker and trying to use it to annotate a Drosophila genome given protein sequences of its closely related species. I have two questions:

1. How maker decide which one to keep if one query protein has two similarly best hits in the target genome, e.g., gene duplication?

2. Is there any way to track the maker gene to its corresponding query proteins through setting up some parameters in maker? Or is it possible to directly let maker name the gene model based on its query protein?

I looked through the previous threads, one possible way seems to use model_gff and map_forward option combined. I guess people more experienced than me using maker might know other ways?

Many thanks!

Qi