Normalized Smith-Waterman Formula

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

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updated 10.1 years ago by Biostar

• written 10.3 years ago by '

1 answer

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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written 10.3 years ago by Jean-Karim Heriche

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