I am not quite sure what kind of category or tags this question should fall under, so I hope people won't mind me leaving them quite vague.

I am currently trying to find a way of using a pipeline for the detection of R-genes (https://github.com/AndolfoG/HRP#1) on the Oak genome. However, unfortunately this pipeline works in a way that requires both a reference genome and reference proteome sequence encoded by the same gene set. A reference proteome is not currently available for Oak.

Now I could generate my own reference proteome using TransDecoder (https://github.com/TransDecoder/TransDecoder/wiki) from a reference transcriptome. But this reference transcriptome was created by another lab and is thus annotated differently. So proteins and genes would have different names.

Is there a way I could reconcile the reference genome and a reference proteome generated from a reference transcriptome created by another lab. Or do they both have to be under the same annotation/ naming scheme from the start? which would make this impossible.