Dear all,

i am performing a motif analysis with MEME (im running universalmotifs() package in R for this) with different sets of sequences. I would like to compare the outputs to see the shared motifs across for example two sets of sequences.

The solutions can be:

1. Use the compare_motifs() function from universalmotif() package which is pretty useful but it starts from a single set of motifs and compare all against all, or one against all. For this i should mark somehow the motifs retrieved from each analyses to see what im comparing to what.

2. Generate a single set of sequences and run MEME directly on it to see the number of matches i get.

I am thus searching for some way to compare the two sets of MEME outputs, possibly with compare_motifs(). I'd want to solve this with solution 1.

Thanks in advance for any help