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The computer program starts with the first window of amino acids and calculates the average of all the hydrophobicity scores in that window. Then the computer program moves down one amino acid and calculates the average of all the hydrophobicity scores in the second window. The y axis represents the hydrophobicity scores and the x axis represents the position in the protein sequence.

Notice that the horizontal axis is scaled to include only those amino acids for which a windowed hydropathy score is computed. The default window size is 9 amino acids. First, each amino acid is given a hydrophobicity score between -4. The Window Position values shown on the x-axis of the graph reflect the average hydropathy of the entire window, with the corresponding amino acid as the middle element of that window. A window size is the number of amino acids whose hydrophobicity scores will be averaged and assigned to the middle amino acid in the window.



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First, each amino acid is given a hydrophobicity score between -4. The authors suggest that, using a window size of , the region of maximal hydrophilicity is likely to be an antigenic site. This pattern continues to the end of the protein, computing the average score for each window and assigning it to the middle amino acid in the window.

The default window size is 9 amino acids. Setting window size to 5-7 is suggested to be a good value for finding putative surface-exposed regions, whereas a window size of 19-21 yields a plot in which transmembrane domains stand out sharply, with values of at least 1. The y axis represents the hydrophobicity scores and the x axis represents the position in the protein sequence. For example, if the window size were 19, the score at window position 10 would be the average hydropathy of the 19 amino acids from position 1 to position 19 in the input sequence. Notice that the horizontal axis is scaled to include only those amino acids for which a windowed hydropathy score is computed.


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