By default, STREME (MEME-suite) uses second-order shuffles of the input sequences as background. STREME highlights its usefulness for CLIP-data, which would be my origin of sequence-inputs. In this context (CLIP-data), each input sequence represents a significant interaction zone (peak) located on bound mRNAs.

As non-peak regions are the background of my inputs, it seems more reasonable to me to use non peak-regions as background for MOTIF search as well.

For this reason, I would like to ask whether someone could give more insights to why this is not the default. I guess the reason must be of mathematical nature.


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