I want to find some upstream regulatory motifs shared commonly in my genes. The case is that the upstream regions of my genes do not often show a high global sequence similarity thus an alignment of all of the sequences is not easy to do. Does anyone have any idea about how to do it? Thanks a lot!
In case you want to do motif finding for a large number of gene clusters it can be a challenge processing all of the results one-by-one. We had this problem in our work and came up with this tool which runs MEME for a number of clusters in parallel and provides a single, interactive output page: