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.
Did you find the solution?