How do I interpret the Scansite score for my site?
Scores in Scansite start at 0.000 if the sequence optimally matches the given motif, and the scores increase for sequences as they diverge from the optimal match. The score histograms and the percentile are the main ways to tell how good a score is for a given motif. If your site ranks in the best 0.2% of all sites, that is quite good (this is the “high stringency” threshold value we use for most of the motifs). The Z score will also tell you how many standard deviations from the mean it is (the Z score will be negative because lower Scansite scores are better). For database searches, the percentile is calculated from all proteins you searched (a whole database, for example). For the Motif Scan program, the percentile is calculated from a reference database search, which is the vertebrate section of the Swiss-Prot database. It may be worthwhile to consider the surface accessibility of the predicted site, as shown by the plot below the graph of sites found. A site that can actually be r
