What does “use foreground, unaligned” (in the background parameters) mean?
Since motif-x creates a pseudo-alignment of FASTA data on a central residue, an appropriate background for a large FASTA data set would be to use the set of all non-centered peptides of a given width as the background. In this way, you can actually use your foreground data set also as your background (this is what we mean by “use foreground, unaligned”). Sometimes this works better, sometimes it does not. We suggest trying several different backgrounds to get optimal results. Also, since using foreground, unaligned can sometimes produce a relatively small background data set, it may be necessary to relax significance thresholds to get back motifs.
