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Unformatted text preview: BCB 567/CprE 548 Fall 2007 Homework 5 Solutions 1. The maximum possible SP score occurs when all sequences are the same. In this case the total score is n k 2 α . This is because each column is perfectly matched: AAAA AAAA .... AAAA The worst possible SP score occurs when each string consists of a single unique character from Σ. In this case, the SP score becomes one of two equations. If all sequences are aligning (for a MSA length of n ), the score is: n k 2 ! β = nk ( k 1) β 2 AAAA BBBB .... KKKK If all sequences are aligned with gaps (total MSA lenght of nk ), the score is: nk ( k 1) γ = nk ( k 1)2 γ 2 = n k 2 ! 2 γ AAAA...BBBB... ......KKKK Either of these cases could have lower total score depending on whether or not β < 2 γ . 1 2. Example: XYX, YXY, and YXX. α = 1 , γ = 2 , β = 1 In this case, the multiple alignment: XYX YXY YXX is optimal with score of 3. However, obviously the pairwise aligment XYX YXY with a score of 3 is not optimal. XYXYXY with a score of 2 is optimal. 2 3. The first thing we should do is generalize the kband to d dimensions. Recall that we defined the kband to be all cells such that  i j ...
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 Fall '06
 OLIVEREULENSTEIN
 Trigraph, Fibonacci number, Alignment, Sequence alignment

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