What is motif-x designed to do?
Initially motif-x was designed to extract phosphorylation motifs from large tandem mass spectrometry-based data sets by making use of the intrinsic alignment of the data around the phosphorylation sites. Since then we have discovered that motif-x is particularly well suited to extracting motifs from practically any sequence based data set, with the simple caveat that the data first needs to be “pseudo-aligned” by centering it on a particular residue (motif-x does this for you, you just need to specify the residue to center on).
