How do I perform discriminative motif discovery using the command line version of MEME?

[CharlesEGrant]

Discriminative motif discovery using MEME is described in this paper:

The value of position-specific priors in motif discovery using MEME
http://www.biomedcentral.com/1471-2105/11/179

In brief, the script 'psp-gen' is used to generate position priors (PSP) from positive and negative sequence sets. The documentation for 'psp-gen' can be found here:

http://meme-suite.org/doc/psp-gen.html

The output format of 'psp-gen' is described here:

http://meme-suite.org/doc/psp-format.html

The output of 'psp-gen' should be saved in a file. MEME is then run on the positive sequence set and MEME's '-psp' option is used to specify the name of the PSP file you generated in the previous step.  The '-psp' option is described in section 'F' of the MEME command line documentation:

http://meme-suite.org/doc/meme.html