I have been trying to run microsynteny for a set of MAPK genes from two plant species using http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf. I have protein sequences of MAPK gene from Arabidopsis and Sunflower. I also have gff file for both genomes including their genome sequences. Can someone please clarify how I can get plots like these: https://www.researchgate.net/figure/Microsynteny-related-to-miR167-families-in-a-Arabidopsis-c-Populus-e-grape-g-rice_fig3_50592226

My questions here are: Do I need to blast protein sequences of each genome against the genome of both Arabidopsis and Sunflower? Or Do I just blast protein sequences of each genome against each other and against self?

Can someone please clarify how to work on this problem? Thanks for your help in advance.