I have two genome assemblies from two phenotypes of a non-model ant species. I have performed gene prediction on them both and have found a difference in the number of predicted genes. How do I find these differing genes? I can't compare gene IDs as they will be different in both assemblies and I can't pull their positions and compare them as the same gene has different coordinates in both assemblies simply due to the assemblies being different.
Any ideas on how I can compare these putative genes between the two genomes?