It seems like it should be possible to use the TOMTOM software (locally installed and running via command line) to quantify motif similarity between motifs discovered via MEME/DREME and a custom set/database of motifs. I am wondering if anyone knows how to do this.
I can see that tomtom runs a command like this:
tomtom -oc tomtom_example_output_files -min-overlap 5 -dist pearson -evalue -thresh 10 -no-ssc STRGGTCAN.meme JASPAR_CORE_2009.meme
in this example the STTRGGCTCAN(?) and JASPAR CORE 2009 databases being specified. Are these .meme databases consisting of motifs in the minimal MEME motif format? I have a custom set of thousands of PFMs in the minimal MEME format, can I run TOMTOM to compare my experimental motifs against these? I was trying to look at the source files of my MEME installation to look at where the .meme database files are being kept but I haven't been able to locate them.
Link to MEME suite: http://meme.nbcr.net/meme/documentation.html
TOMTOM paper: http://genomebiology.com/2007/8/2/r24
Minimal MEME format: http://meme.nbcr.net/meme/examples/sample-dna-motif.meme-io
Many thanks for any advice you can give :)