Working with peptides/proteins

[StLeonidas]

I have successfully tested YAMDA searching motifs in the test DNA dataset. Then I tried to run YAMDA with aminoacidic data (like an example in attached logo figure) with obvious motif. I have tried to lower thresholds and soften cut-off with run_em.py options but no luck. What is obstructing the detection of motifs in the protein dataset? Could you recommend a way or options set allowing to get motifs in such cases?