Searching for two adjacent motifs in a list of input sequences

[Roberto Avellino]

Hi,

I have a motif sequence (Motif X) that is highly represented in my list of input sequences. The next question I have is that I want to add an additional layer of analysis where I specifically ask : what is the chance that an additional motif sequence Y occurs adjacent to motif X in my input sequences. Which is the best tool for this?

Thanks

Roberto

[cegrant]

I don't think the MEME Suite has a tool that does exactly what you seem to be asking for. SpaMo seems to be the closet to what you are looking for. SpaMo identifies the most common spacing between a primary motif and a secondary motif. It can consider multiple secondary motifs in one run.

Other tools that might be relevant are:

MAST identifies sequences that contain good matches to all members of a set of motifs.

MCAST scans sequences for clusters of co-occuring motifs.

GLAM2 performs de novo discovery of motifs that contain gaps

GLAM2Scan scans sequences for gapped motifs identified by GLAM2

But I don't think any of those are really what you are looking for.