Hydrophobicity Grapher graphs the hydrophobicity/hydrophilicity of a sequence of amino acids, using a sliding window. The window size can be specified by the user, and several hydrophobicity scales can be used to determine the plot.
Because of how the plot is calculated, the very beginning and very end of the sequence will be cut off. The amount cut off will depend on the window size: exactly one half of the window size will be deleted from the beginning of the sequence, and the same amount will be cut off the end. Therefore, if one has a window size of 20, the first and last 10 amino acids will not be plotted.
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Kyte J, Doolittle RF.
A simple method for displaying the hydropathic character of a protein. J Mol Biol. 1982 May 5;157(1):105-32.
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A computer program for predicting protein antigenic determinants. Mol Immunol. 1983 Apr;20(4):483-9.
Parker JM, Guo D, Hodges RS.
New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry. 1986 Sep 23;25(19):5425-32.