I have a set of 5kb sequences upstream of a gene from different primates, and I would like to know what motifs are in enhancers and promoters of primates vs the 5kb upstream sequences of a set of the same gene but for rodents.
Would the analysis with MEME suite be correct with the “Discriminative mode”, and putting the rodent sequences in control sequences and the primate sequences in the primary sequences? To contrast, since the normal method looks for similarities.
I think the discriminative mode is more to look for enrichment of the same motif. But different species may have the same motif with different information values.
So one thought is, given sets of orthologous genes, you might perhaps perform a MEME scan for conserved motifs over their respective upstream promoter sequences. Pairs of per-species MEME PWMs could be compared with TOMTOM to query for significantly similar motifs. Putting results into a grid could help with comparing all species pairings at a glance.
Another thought is to use existing (MEME-formatted) PWMs with FIMO to generate whole-genome scans for published motifs, comparing hits over ortholog promoter regions.