bookmark pepwindow Draws a hydropathy plot for a protein sequence. pepwindow draws a classic Kyte & Doolittle hydropathy plot for a protein sequence. It calculates hydropathy in windows of a specified size over the input sequence. Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensemble. Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application.