Questions RE:Sequence Masking in Fimo

[Sam Lambert]

Hi there,

I'm wondering how FIMO handles N-masked sequences? Does it just scan over these or does it treat it as the highest scoring base? Also how does it handle soft-masked sequences like lower-case letters? I guess I'd also like to know of this is the same for MAST

[James Johnson]

I believe that both FIMO and MAST will not match motifs to positions that contain ambiguous characters (which includes N). Currently no tools in the MEME Suite make any distinction based on the case of the letters in FASTA sequences.