Affine Gap Alignment (y’know, the one with σ and ε)

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Presentation transcript:

Affine Gap Alignment (y’know, the one with σ and ε)

Why? Realism Control Readability Consider: String 1: ACCCCCCCCCA String 2: ATCCTA Why?

What changes could transform string 1 into string 2? Scenario 1: Insert Ts Delete Cs String 1: ACCCCCCCCCA String 2: ATCCTA

What changes could transform string 1 into string 2? Scenario 2: Transform Cs to Ts Delete Cs String 1: ACCCCCCCCCA String 2: ATCCTA

What changes could transform string 1 into string 2? String 1: ACCCCCCCCCA String 2: ATCCTA Scenario 3: All Cs are deleted TCCT is inserted

All gaps created equal <—

-σ = - 1 -ε = - 1 Which scenario does this reflect?

Some gaps more equal than others <—

-σ = - 2 -ε = - 1 Which Scenario does this reflect?

How though? Six tables Initial middle Triple loop Backtrack as [source table, direction] How though?

HAGS