What is the background parameter?
The background parameter is used to calculate the amino acid frequency distribution in background data. motif-x calculates this distribution dynamically throughout the motif building process, and this is at the heart of why motif-x is successful at extracting biologically relevant motifs. If you have a tandem mass spectrometry-based phosphorylation data set that came from yeast, then a yeast background should be selected. If you do not see an appropriate background from our list, then you can always upload your own background data set.
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