meme mast overlapping motif search

[Varsha Sundaresan]

Hi, I am using meme mast suite for motif scanning and the manual says that mast only gives output of non-overlapping sequences. I feel like I might be missing some potential motif hits because of this and was wondering if there is a way to make mast output the overlapping hits as well? I appreciate your help.

[CharlesEGrant]

You don't specify what analysis you are trying to perform, but based on your question I suspect you should be using FIMO rather than MAST. This posting may be helpful:  How Does MAST differ from FIMO.

[Varsha Sundaresan]

Hi Charles, I am trying to perform motif scanning using MAST, to obtain a list of matches in the genome. I can use FIMO too, but do any of them give the hits in the overlapping motifs in the genome? For eg, if the 2nd TF binding motif match (lets say 20bp) overlaps with the 1st motif match by a bp or 2 mast gives only the 1st motif coordinates in the output and not motifs with 0 spacer or overlapping motifs. Would FIMO work for identifying such overlapping motifs? Thanks for your help.

[CharlesEGrant]

FIMO would be the tool for this analysis. It considers each motif independently, and scores each position in the sequences independently, so overlaps are not an issue. MAST identifies non-overlapping instances of motifs as a side effect, and the -hit_list option can report them, but it's not really what MAST is for. MAST is designed to assign to evaluate the overall match between a sequence and a set of motifs.

[Varsha Sundaresan]

HI Charles, I will try out FIMO. Thank you so much!