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  • The gap in w (gray background) is inserted to align the profiles and is not part of Y. Consider the SP ...b(y) = g/2 (1 - f yo) (1 + hw(y)H), (12)t(y) = g/2 (1 - f yc) (1 + hw(y)H). (13)Here, g is a parameter that can be considered a default per-gap penalty, hw(y) is 1 if y falls within a window of w consecutive hydrophobic residues or zero otherwise, and H is a tunable parameter.
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