When the line is in the upper part of the frame, it indicates a hydrophobic region, and when the line is in the lower half, a hydrophilic region. The plot may be used to spot putative membrane-buried segments and exposed parts such as antigenic determinants, or to compare distantly related sequences to see if some charactersitic pattern of hydrophobicity has been preserved.
PepWindow plots default to a running average curve.
Care should be taken when using this plot as it increases the contrast of the data but provides no image enhancement. PepWindow uses a default window of 9. Mesh values from 2 to 25 are allowed. The input file for PepWindow is a protein sequence file. See Chapter 5, Using Graphics in the User's Guide for more information about configuring your process for graphics.