I have predicted enhancers for 6 genes. I want to compare these enhancers with each other to find a subset out of all these which are similar to each other in terms of the motifs that they have. All I find are methods that do a pairwise comparison (such as D2z) between enhancers but I don't find that informative as I want enhancers which are similar from all 6 genes. Does any one know any methods that can accomplish that? or is it possible to extract from pairwise output such as D2z the enhancers from 6 genes that are all similar to each other?
Thanks a lot aravind!
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