How are the background frequencies in motif files used?

[CharlesEGrant]

The background frequencies in the motif file are used when you provide one of either the letter-probability matrix or log-odds matrix but not the other, in which case it uses the motif background to convert into the other. If you are providing the letter-probability matrix then the motif background will have no impact on the running of most MEME Suite programs (because only MAST uses the log-odds matrix in the motif file) unless you specify the special value "--motif--" as the background file. 

Whatever you specify as the background file will be used to apply pseudocounts and convert into a log score matrix for the actual computation. 

Special values for the background file are: 
--nrdb-- this uses the hard coded NRDB background 
--uniform-- this uses a uniform background 
--motif-- this uses the background in the motif file (note "motif-file" also works but it's only intended for backwards compatibility so don't use it) 

If you don't specify a background file it will use the hard coded NRDB values not the motif background. 

For reference the NRDB values are: 
For DNA: 
A=0.281774, C=0.222020, G=0.228876, T=0.267330 
For protein: 
A=0.073164, C=0.018163, D=0.051739, E=0.062340, F=0.040283, G=0.069328, H=0.022428, I=0.056282, K=0.058493, L=0.091712, M=0.023067, N=0.046077, P=0.050674, Q=0.040755, R=0.051897, S=0.073802, T=0.059411, V=0.064362, W=0.013341, Y=0.032682 

Future releases of the MEME Suite (> v4.7.0) will allow you to leave out the background from the minimal MEME format. In that case where the motif background is required a uniform background will be used. That feature was meant to be in the current release (4.7.0) but a bug causes it to crash instead so for the moment the motif background is required.