If I got the tool right, one use case would be similarity search.

So you just finished the brand new genome sequencing of Sugarcane for example.

And you are interested in Aluminium resistence genes to be able to plant sugarcane in aluminium packed soils that would normally kill the plant.

What you do is to throw parts of the genome in a tool like that (there are others) and see if you can find a match for a Sorghum(Wheat,Corn...) Aluminium resistence gene that has been already researched and tested. The closest related the better.

Now you have some clue about where to start your studies or which genes you should be looking for in your new varieties or which gene to try to insert in your next Agrobacterium or gene bombardment test.

Cheers.

PS: I left the Bioinformatics field a few years ago (best job I ever had BTW) So correct me if I am wrong.