I'm working on a fungus species, on which I have two genome assemblies, performed on two different strains, and also one annotation for each assembly.
By crossing the annotations peptide sequences results, with BDBH analysis, I get some common proteins, and some specific to each strain.
I know, by blasting them on genomes assembly, that most of the "strain specifics" genes are however also present on the other strain genome. (certainly due to the different annotation software)
What I would like to do is to retrieve the sequences of one strain specifics genes on the other strain genomes, so that I complete the annotation.
Would anybody have a clue on how doing such a thing?