Looking for advice on chosing Meme-suit function

[Le Dong]

Dear all,

I am looking for a way to analyze a set of gene promoters that come from the same species. I would like to compare these promoter sequences to determine whether or not they share any common binding motifs for a specific transcription factor.

While researching, I came across a recommendation to use XTREME for this task. I would appreciate hearing everyone's thoughts and recommendations on this approach.

Many thanks.

[cegrant]

The tools in the MEME Suite fall into 4 general categories: de novo motif discovery (STREME and MEME), motif match scanning (FIMO), motif enrichment (SEA, AME, and CENTRIMO), and motif comparison (TOMCAT). XSTREME runs STEME, MEME SEA, FIMO, and TOMCAT in a single command.

Do you have a position weight matrix for your transcription factor? If so then de novo motif discover wouldn't seem to be necessary, and you could go straight to FIMO and SEA. If you expect your promoter sequences to bind multiple TF in common you might consider MAST which scores sequences for matches to a collection of motifs rather than a single motifs.

If you don't have a position weight matrix for your transcription factor then XSTREME would be a good place to start.