Why can't FIMO from the MEME suite score sequences with 'any nucleotide' DNA characters (ex. N)? Can I use MAST tool instead?

Question

[Jillian]

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!

[Mensur Dlakic]

I don't know the answer to your FIMO question, but MAST can be used to get p-values for motif scanning.