What is the central character parameter?
Since motif-x was initially designed to extract motifs from large data sets of modified peptides (usually phosphorylated tryptic peptides generated by large-scale tandem mass spectrometry experiments), the central character initially meant the modified residue. Now however, we realize that motif-x can actually extract motifs from any data set, but it still requires a residue on which to create a “pseudo-alignment” of the data. Note that the central character is case-sensitive, and must be a character that is actually found in the data set.
