Normalized Smith-Waterman Formula
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6.8 years ago
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I found the following formula for normalizing Smith-Waterman scores, I know that p1 and p2 refer to first and second proteins, but I do not understand what SW(p1,p2) refers to. Can somebody please explain?

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smith-waterman • 2.0k views
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Entering edit mode
6.8 years ago

Hard to tell without context but my guess is that SW stands for Smith-Waterman so you normalize the score by the product of the square roots of the score of each protein aligned to itself.

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