I have a set of around 250 genes which I'm testing and among everything I am trying I also decided to check if they're enriched for particular GO Terms or gene families. Sadly, I am not working with a well annotated organism, so my GO Term mapping on my genes actually returned only 20% of the genes as covered by GO Terms.
What should someone do in these situations? Are there any tools that try to extend the GO Term coverage with some particular (idk, just guessing) homology modelling?
Also, do you have any suggestions on other tests that I should/could do? I have the functional annotation for each of these sequences, so I am now manually checking the annotated function but I would like to know if there are cool tools to do that automatically.