Hello, I am trying to understand why FIMO --a motif scanning tool that's a part of the MEME suite tools---cant score DNA sequences with ambiguous characters? I understand MAST (also a MEME tool) is for scoring homologous sequences based on their motif p-values, BUT it is able to handle ambiguous characters in the DNA sequence....can I just use MAST instead to get the motif's p-value in my sequences?

thanks for your patience!