I am running a cross-species motif analysis using FIMO with motifs from the JASPAR database. I noticed that when you convert the PWM to MEME format using the jaspar2meme command, there is an option to use a background file in a HMM format to parse against the motif so that it contains the background frequencies. But there is a similar option available when running the motif analysis as you can also get the background frequencies using the fimo -bg in -options

Would someone be able to advice me on whether there is a difference between these commands? Should both commands be used?

I know I will need to run multiple background searches as I am using different species so any help would be greatly appreciated.